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

Inheritance diagram for roiRegion:

Collaboration diagram for roiRegion:

Public Member Functions
	roiRegion (hImg)
	Constructor for the class. More...

function	clearContents ()
	Set all elements of the class to default values. More...

function	addROI (handles, type, index, coordinates, noPoints)
	Adds ROI. More...

function	imfreehandFun (handles, index)
	Adds impoly type of ROI using imfreehand tool. More...

function	impolyFun (handles, index, coordinates, noPoints)
	Adds impoly type of ROI. More...

function	imrectFun (handles, index, coordinates)
	Adds imrect type of ROI. More...

function	imellipseFun (handles, index, coordinates)
	Adds imellipse type of ROI. More...

function	storeROI (newData, index)
	add or insert ROI information into the obj.Data structure More...

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

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

function	setDefaultOptions ()
	Set all values of the Options structure of the class to default values. More...

function	updateOptions ()
	Update the Options structure of the class. More...

function	resample (resampledRatio)
	Recalculation of ROI position during image resampling. More...

function	crop (cropF)
	Recalculation of ROI position during image crop. More...

function [ position , screenPosition ] =	drawROI (handles, type, pos, instant)
	draw a ROI object in the handles.imageAxes More...

function	updateROIposition1 (new_position)
	Update ROI position during movement of imrect and imellipse. More...

function	updateROIposition2 (new_position)
	Update position during movement of impoly, imline. More...

function handles =	addROIsToPlot (handles, mode)
	plot ROIs above the imageAxes of im_browser More...

function mask =	returnMask (index, Height, Width, orient, blockModeSwitch)
	Return a bitmap mask of the specified ROI. More...

function	updateROIScreenPosition (mode)
	Updates position of ROI when plotting in handles.imageAxes. More...

Public Attributes
	roi
	a structure with ROI data: More...

	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` More...

	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; More...

	hImg
	handle to imageData class More...

Detailed Description

class is resposnible to keep regions of interest (ROI)

Constructor & Destructor Documentation

roiRegion.roiRegion ( hImg )

Constructor for the class.

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

Parameters

hImg	- handle to imageData class

References hImg.

Member Function Documentation

function roiRegion.addROI	(	handles,
		type,
		index,
		coordinates,
		noPoints
	)

Adds ROI.

Parameters

handles	handles structure of im_browser
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:

handles.Img{handles.Id}.I.hROI.addROI(handles, 'imrect'); // Add a new imrect ROI

handles.Img{handles.Id}.I.hROI.addROI(handles, [], 3); // Modify the 3rd ROI

function handles = roiRegion.addROIsToPlot	(	handles,
		mode
	)

plot ROIs above the imageAxes of im_browser

Parameters

handles	handles structure of im_browser.m
mode	a string that defines a mode of the shown image: `shown` (in most cases), or `full` (for panning)

Required fields of handles:

Examples:

handles = handles.Img{handles.Id}.I.hMeasure.addROIsToPlot(handles, 'shown'); // to show the measurements above the image in the imageData.plotImage function

handles = handles.Img{handles.Id}.I.hMeasure.addROIsToPlot(handles, 'full'); // to show the measurements above the image in the im_browser_WindowButtonDownFcn function

function roiRegion.clearContents ( )

Set all elements of the class to default values.

Examples:

roiRegion.clearContents();

clearContents(obj); // Call within the class

Examples:

roiRegion.clearData();

clearData(obj); // Call within the class

Examples:

handles.Img{handles.Id}.I.hROI.findIndexByLabel('ROI 1'); // Return index of the ROI that has 'ROI 1' label

function roiRegion.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 = roiRegion.crop(cropF); // crop ROIs

indices = remove(obj, cropF); // Call within the class; crop ROIs

function [ position , screenPosition ] = roiRegion.drawROI	(	handles,
		type,
		pos,
		instant
	)

draw a ROI object in the handles.imageAxes

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

Parameters

handles	handles structure of im_browser.m
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 handles:

Examples:

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

position = drawROI(obj, handles, 'imline', [10, 10; 50, 50]);; // Call within the class; draw a line

function [ number , indices ] = roiRegion.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 = roiRegion.getNumberOfROI(4); // get the total number of ROIs for the XY orientation

number = getNumberOfROI(obj); // Call within the class; get the total number

function roiRegion.imellipseFun	(	handles,
		index,
		coordinates
	)

Adds imellipse type of ROI.

Parameters

handles	handles structure of im_browser
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 handles:

Examples:

handles.Img{handles.Id}.I.hROI.imellipseFun(handles, 5); // Add a new imellipse ROI to position 5

handles.Img{handles.Id}.I.hROI.imellipseFun(handles, 5, [100, 150, 250, 350]); // Add a new imellipse ROI to position 5; x1=100, x2=150, radiusX=250; radiusY=350

References getClickPoint().

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function roiRegion.imfreehandFun	(	handles,
		index
	)

Adds impoly type of ROI using imfreehand tool.

Parameters

handles	handles structure of im_browser
index	index of the ROI. If not empty will allow to modify a ROI with the provided index

Examples:

handles.Img{handles.Id}.I.hROI.imfreehandFun(handles, 5); // Add a new impoly ROI to position 5

References mib_inputdlg().

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function roiRegion.impolyFun	(	handles,
		index,
		coordinates,
		noPoints
	)

Adds impoly type of ROI.

Parameters

handles	handles structure of im_browser
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 handles:

Examples:

handles.Img{handles.Id}.I.hROI.impolyFun(handles, [], [], 5); // Add a new impoly ROI with 5 vertices

handles.Img{handles.Id}.I.hROI.impolyFun(handles, 5, [100, 150; 250, 350; 50, 150]); // Add impoly ROI to position 5; with specified vertices

References getClickPoint().

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function roiRegion.imrectFun	(	handles,
		index,
		coordinates
	)

Adds imrect type of ROI.

Parameters

handles	handles structure of im_browser
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 handles:

Examples:

handles.Img{handles.Id}.I.hROI.imrectFun(handles, 5); // Add a new imrect ROI to position 5

handles.Img{handles.Id}.I.hROI.imrectFun(handles, 5, [100, 150, 250, 350]); // Add a new imrect ROI to position 5; x1=100, x2=150, width=250; height=350

References getClickPoint().

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function roiRegion.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

function roiRegion.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 = roiRegion.resample(resampledRatio); // resample ROIs

indices = resample(obj, resampledRatio); // Call within the class; resample ROIs

function mask = roiRegion.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 = roiRegion.returnMask(new_position, 1); // get mask of ROI number 1

mask = returnMask(obj, 0); // Call within the class; get combined mask of all shown ROIs

References ib_connectPoints().

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function roiRegion.setDefaultOptions ( )

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

Examples:

roiRegion.setDefaultOptions();

setDefaultOptions(obj); // Call within the class

function roiRegion.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
n	[optional] position where to add the measurement, default - number of measurements in obj.Data + 1

Examples:

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

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

function roiRegion.updateOptions ( )

Update the Options structure of the class.

Examples:

handles.Img{handles.Id}.I.hROI.updateOptions();

updateOptions(obj); // Call within the class

function roiRegion.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]

function roiRegion.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]

function roiRegion.updateROIScreenPosition ( mode )

Updates position of ROI when plotting in handles.imageAxes.

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

updateROIScreenPosition(obj, 'full'); // Call within the class; update positions of all ROIs during panning

Member Data Documentation

roiRegion.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

Referenced by mibmeasureTool>saveBtn_Callback(), and roiSaveBtn_Callback().

roiRegion.hImg

handle to imageData class

Referenced by roiRegion().

roiRegion.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;

Referenced by classRF_train(), get_black_white_filter(), ib_anisotropicDiffusion(), menuModelsSaveAs(), model_cm_Callback(), and regRF_train().

roiRegion.roi

a structure with ROI data:

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

Referenced by do_andiff_filtering(), do_andiff_filtering_backup(), do_diplib_andiff_filtering(), ib_anisotropicDiffusion(), ib_autoBrightness(), ib_linearContrast(), ib_smoothImage(), imageFilterDoitBtn_Callback(), menuImageIntensity(), menuImageProfileArbitrary_Callback(), menuImageProfileLine_Callback(), menuMaskInvert(), menuSelectionInvert(), and menuToolsMeasure().

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

Classes/@roiRegion/roiRegion.m

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation