class is responsible for keeping Measurements More...

Inheritance diagram for mibMeasure:

Collaboration diagram for mibMeasure:

Public Member Functions
	mibMeasure (hImg)
	Constructor for the class.

function	addMeasurements (newData, n)
	add or insert measurement into the obj.Data structure

function	addMeasurementsToPlot (mibModel, mode, axes)
	plot measurement marks above images

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

function	clearData ()
	Removes all values of the Data structure.

function	generateKymograph (mibController, index, colCh, options)
	generate kymograph and save it as an image

function	editMeasurements (mibController, index, colCh, widthProfile, finetuneCheck, calcIntensity)
	update measurements

function	removeMeasurements (index)
	removeMeasurements(obj, index) Remove measurement(s) from the class

function	setOptions ()
	Update all values of the Options structure of the class.

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

function position =	drawROI (mibController, type, pos, instant)
	show a ROI object in the mibController.mibView.handles.mibImageAxes for selection of the area to measure

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

function number =	getNumberOfMeasurements ()
	number = getNumberOfMeasurements(obj) Get number of stored measurements

function circ =	circlefit (x, y)
	least squares circle fitting (see matlab help/demo (pendulum))

function result =	AngleFun (mibController, index, colCh, finetuneCheck, calcIntensity)
	This function allows the measurement of an angle between 3 points.

function result =	CaliperFun (mibController, index, colCh, finetuneCheck, calcIntensity)
	measuring a distance between two opposite sides of an object

function result =	CircleFun (mibController, index, colCh, finetuneCheck, calcIntensity)
	This function allows the measurement of a radius.

function result =	DistanceFreeFun (mibController, colCh, finetuneCheck, calcIntensity, freehandOptions)
	measuring of distance along the free-hand path. The path is converted to the impoly line

function result =	DistancePolyFun (mibController, index, colCh, noPoints, finetuneCheck, calcIntensity, options)
	measuring of distance along the path

function result =	PointFun (mibController, index, colCh, finetuneCheck, calcIntensity)
	add a point as a marker

function result =	DistanceFun (mibController, index, colCh, finetuneCheck, integrateWidth, calcIntensity, options)
	measuring distance between two points

Public Attributes
	Data
	a structure with measurements .Data.n - index, double .Data.type - type, string: `LinDistance`, .Data.value - value, double .Data.info - info, free text .Data.X - X-coordinates of points .Data.Y - Y-coordinates of points .Data.Z - Z-coordinates of points .Data.T - T-coordinates of points .Data.orientation - orientation of the measurement: 4-yx; 1-zx; 2-zy .Data.spline .Data.circ .Data.intensity - average intensity of the profile .Data.profile - intensity profile .Data.integrateWidth - only for Distance (linear) width of the integrated intensity profile, otherwise empty

	hImg
	handle to mibImage class

	Options
	a structure with show options .Options.marker1 = `o`; - style 1 for markers .Options.marker2 = `.`; - style 2 for markers .Options.markersize = `10`; - size of markers .Options.linestyle1 = `-`; - style 1 for lines .Options.linestyle2 = `–`; - style 2 for lines .Options.linewidth = `1` ; - width for lines .Options.color1 = `y`; - color style 1 .Options.color2 = `k`; - color style 2 .Options.textcolorfg = `y`; - text color .Options.textcolorbg = `none`; - color for text background .Options.fontsize = `14`; - size of the font .Options.splinemethod = `spline`; - method for splines .Options.showMarkers = 1; .Options.showLines = 1; .Options.showText = 1;

	roi
	a structure with ROI data:

	typeToShow
	a string that defines type of measurements to show:

	fixZ
	a switch that fixes Z and T values when the measurements are recalculated

EVENT	addMeasurement
	add a new measurement, when the Measure Tool is displayed note: use this syntax instead to send event motifyEvent.Name = `addMeasurement`; eventdata = ToggleEventData(motifyEvent); notify(obj.mibModel, `modelNotify`, eventdata);

EVENT	updatePosition
	update coordinates of measurements

Detailed Description

class is responsible for keeping Measurements

Constructor & Destructor Documentation

◆ mibMeasure()

mibMeasure.mibMeasure ( hImg )

Constructor for the class.

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

Parameters

hImg	- handle to mibImage class

References hImg.

Member Function Documentation

◆ addMeasurements()

function mibMeasure.addMeasurements	(		newData,
			n )

add or insert measurement 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:

mibMeasure.addMeasurements(newData, 5); insert measurement to position 5

mibMeasure.mibMeasure

mibMeasure(hImg)

Constructor for the class.

Definition mibMeasure.m:134

References n.

◆ addMeasurementsToPlot()

function mibMeasure.addMeasurementsToPlot	(	mibModel,
		mode,
		axes )

plot measurement marks above images

Parameters

mibModel	mibModel class of MIB
mode	a string that defines a mode of the shown image: `shown` (in most cases), or `full` (for panning)
axes	define a handles to axes that should be used for drawing, used in mibSnapshotGUI.m; default mibView.handles.mibImageAxes

Required fields of mibModel:

Examples:

obj.mibModel.I{obj.mibModel.I}.hMeasure.addMeasurementsToPlot(obj.mibModel, 'shown', obj.mibView.handles.mibImageAxes); // call from mibController; to show the measurements above the image in the mibController.plotImage function

obj.mibModel.I{obj.mibModel.I}.hMeasure.addMeasurementsToPlot(obj.mibModel, 'full', obj.mibView.handles.mibImageAxes); // call from mibController; to show the measurements above the image in the mibGUI_WindowButtonDownFcn function

References mibModel.convertDataToMouseCoordinates(), and mibModel.mibShowAnnotationsCheck.

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◆ AngleFun()

function result = mibMeasure.AngleFun	(	mibController,
		index,
		colCh,
		finetuneCheck,
		calcIntensity )

This function allows the measurement of an angle between 3 points.

Parameters

mibController	handle of mibController
index	[Optional] an index of measurement to update; when empty ([] ) - adds a new measurement
colCh	[optional] color channel to use for profile; default = 1
finetuneCheck	[optional] 1 (default) - allow fine-tuning during the placing of measurements; 0 - instant placing
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate

Return values

calcIntensity result - 1-success, 0-cancel

Required fields of mibController:

Examples

obj.mibModel.I{obj.mibModel.Id}.hMeasure.AngleFun(obj, [], 1); // call from mibMeasureToolController; get points and measure the angle between them. Calculate intensity profile for color channel 1

obj.mibModel.I{obj.mibModel.Id}.hMeasure.AngleFun(obj, 2, 1); // call from mibMeasureToolController; edit second measurement.

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

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◆ CaliperFun()

function result = mibMeasure.CaliperFun	(	mibController,
		index,
		colCh,
		finetuneCheck,
		calcIntensity )

measuring a distance between two opposite sides of an object

Parameters

mibController	handle of mibController
index	[Optional] an index of measurement to update; when empty ([] ) - adds a new measurement
colCh	[optional] color channel to use for profile; default = 1
finetuneCheck	[optional] 1 (default) - allow fine-tuning during the placing of measurements; 0 - instant placing
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate

Return values

calcIntensity result - 1-success, 0-cancel

Required fields of mibController:

Examples

obj.mibModel.I{obj.mibModel.Id}.hMeasure.CaliperFun(obj, [], 1); // call from mibMeasureToolController; get points and measure the distance between them. Calculate intensity profile for color channel 1

obj.mibModel.I{obj.mibModel.Id}.hMeasure.CaliperFun(obj, 2, 1); // call from mibMeasureToolController; edit second measurement.

References D(), max, mibController.mibModel, mibController.mibView, n, and mibController.plotImage().

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◆ circlefit()

function circ = mibMeasure.circlefit	(		x,
			y )

least squares circle fitting (see matlab help/demo (pendulum))

Parameters

x
y

Return values

circ

Generated fields of circ:

References M, and n.

◆ CircleFun()

function result = mibMeasure.CircleFun	(	mibController,
		index,
		colCh,
		finetuneCheck,
		calcIntensity )

This function allows the measurement of a radius.

Parameters

mibController	handle of mibController
index	[Optional] an index of measurement to update; when empty ([] ) - adds a new measurement
colCh	[optional] color channel to use for profile; default = 1
finetuneCheck	[optional] 1 (default) - allow fine-tuning during the placing of measurements; 0 - instant placing
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate

Return values

calcIntensity result - 1-success, 0-cancel

Required fields of mibController:

Examples

obj.mibModel.I{obj.mibModel.Id}.hMeasure.CircleFun(obj, [], 1); // call from mibMeasureToolController; get points and measure the radius. Calculate intensity profile for color channel 1

obj.mibModel.I{obj.mibModel.Id}.hMeasure.CircleFun(obj, 2, 1); // call from mibMeasureToolController; edit second measurement.

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

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◆ clearContents()

function mibMeasure.clearContents ( )

Set all elements of the class to default values.

Examples:

obj.mibModel.I{obj.mibModel.I}.hMeasure.clearContents(); // call from mibController;

◆ clearData()

function mibMeasure.clearData ( )

Removes all values of the Data structure.

Examples:

obj.mibModel.I{obj.mibModel.I}.hMeasure.clearData(); // call from mibController;

◆ DistanceFreeFun()

function result = mibMeasure.DistanceFreeFun	(	mibController,
		colCh,
		finetuneCheck,
		calcIntensity,
		freehandOptions )

measuring of distance along the free-hand path. The path is converted to the impoly line

Parameters

mibController	handle of mibController
colCh	[optional] color channel to use for profile; default = 1
finetuneCheck	[optional] 1 (default) - allow fine-tuning during the placing of measurements; 0 - instant placing
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate
freehandOptions	structure with additional parameters .fixNumberPoints - logical, when checked do not ask for number of points .noPointsEdit - string with selected number of points to use

Return values

freehandOptions result - 1-success, 0-cancel

Required fields of mibController:

Required fields of freehandOptions:

Examples

obj.mibModel.I{obj.mibModel.Id}.hMeasure.DistanceFreeFun(obj, 1); // call from mibMeasureToolController; draw a path and measure the distance between points. Calculate intensity profile for color channel 1

References mibInputMultiDlg(), mibController.mibModel, n, and mibController.plotImage().

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◆ DistanceFun()

function result = mibMeasure.DistanceFun	(	mibController,
		index,
		colCh,
		finetuneCheck,
		integrateWidth,
		calcIntensity,
		options )

measuring distance between two points

Parameters

mibController	handle of mibController
index	[Optional] an index of measurement to update; when empty ([] ) - adds a new measurement
colCh	[optional] color channel to use for profile; default = 1
finetuneCheck	[optional] 1 (default) - allow fine-tuning during the placing of measurements; 0 - instant placing
integrateWidth	[optional] a number of pixels for integration of image intensity profile
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate
options	structure with additional options .widthProfile - width of profile for measurements of intensity profiles, could be empty .outputFilename - full path to the output file .outputFormat - output format, `tif`, csv, mat, preview', when preview show it as a plot .calcKymograph - true/false, calculate kymograph .addScale - add scale to kymograph

Return values

options result - 1-success, 0-cancel

Required fields of mibController:

Required fields of options:

Examples

obj.mibModel.I{obj.mibModel.Id}.hMeasure.DistanceFun(obj, [], 1); // call from mibMeasureToolController; get points and measure the distance between them. Calculate intensity profile for color channel 1

obj.mibModel.I{obj.mibModel.Id}.hMeasure.DistanceFun(obj, 2, 1); // call from mibMeasureToolController; edit second measurement.

References A(), B(), max, mibAddScaleBar(), mibAddText2Img(), mibImageProfileIntegrate(), mibController.mibModel, mibController.mibView, n, and mibController.plotImage().

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◆ DistancePolyFun()

function result = mibMeasure.DistancePolyFun	(	mibController,
		index,
		colCh,
		noPoints,
		finetuneCheck,
		calcIntensity,
		options )

measuring of distance along the path

Parameters

mibController	handle of mibController
index	[Optional] an index of measurement to update; when empty ([] ) - adds a new measurement
colCh	[optional] color channel to use for profile; default = 1
noPoints	[optional] define number of points in the path; default = 5
finetuneCheck	[optional] 1 (default) - allow fine-tuning during the placing of measurements; 0 - instant placing
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate
options	structure with additional options .widthProfile - width of profile for measurements of intensity profiles, could be empty .outputFilename - full path to the output file .outputFormat - output format, `tif`, csv, mat, preview', when preview show it as a plot .calcKymograph - true/false, calculate kymograph .addScale - add scale to kymograph

Return values

options result - 1-success, 0-cancel

Required fields of mibController:

Required fields of options:

Examples

obj.mibModel.I{obj.mibModel.Id}.hMeasure.DistancePolyFun(obj, [], 1, 10); // call from mibMeasureToolController; get 10 points and measure the distance between them. Calculate intensity profile for color channel 1

obj.mibModel.I{obj.mibModel.Id}.hMeasure.DistancePolyFun(obj, 2, 1); // call from mibMeasureToolController; edit second measurement.

References max, mibAddScaleBar(), mibAddText2Img(), mibController.mibGUI_ScrollWheelFcn(), mibController.mibModel, mibController.mibView, N, n, and mibController.plotImage().

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◆ drawROI()

function position = mibMeasure.drawROI	(	mibController,
		type,
		pos,
		instant )

show a ROI object in the mibController.mibView.handles.mibImageAxes for selection of the area to measure

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

Parameters

mibController	a handle of mibController class
type	a type of ROI: 'imline', 'imellipse'
pos	coordinates of the ROI [x1, y1; x2, y2] -> 'imline' [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

Required fields of mibController:

Examples:

position = obj.mibModel.I{obj.mibModel.I}.hMeasure.drawROI(obj, 'imline', [10, 10; 50, 50]); // call from mibController; draw a line

References mibController.mibModel, and mibController.mibView.

◆ editMeasurements()

function mibMeasure.editMeasurements	(	mibController,
		index,
		colCh,
		widthProfile,
		finetuneCheck,
		calcIntensity )

update measurements

Parameters

mibController	handle to mibController class
index	an index of the measurement to update
colCh	number of a color channel for intensity profile, or 0 for all color channels
widthProfile	[optional] width of profile for measurements of intensity profiles, could be empty
finetuneCheck	[optional] a number 0 - do not fine tune the measurement; 1-do the finetuning manually
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate

References mibController.mibModel.

◆ generateKymograph()

function mibMeasure.generateKymograph	(	mibController,
		index,
		colCh,
		options )

generate kymograph and save it as an image

Parameters

mibController	handle to mibController class
index	an index of the measurement to update
colCh	number of a color channel for intensity profile, or 0 for all color channels
options	structure with additional options .widthProfile - width of profile for measurements of intensity profiles, could be empty .outputFilename - full path to the output file .outputFormat - output format, `tif`, `csv, mat` .calcKymograph - true/false, calculate kymograph

Required fields of options:

◆ getNumberOfMeasurements()

function number = mibMeasure.getNumberOfMeasurements ( )

number = getNumberOfMeasurements(obj) Get number of stored measurements

Return values

number number of stored measurements

Examples

number = obj.mibModel.I{obj.mibModel.I}.hMeasure.getNumberOfMeasurements(); // call from mibController; get the total number

◆ PointFun()

function result = mibMeasure.PointFun	(	mibController,
		index,
		colCh,
		finetuneCheck,
		calcIntensity )

add a point as a marker

Parameters

mibController	handle of mibController
index	[Optional] an index of measurement to update; when empty ([] ) - adds a new measurement
colCh	[optional] color channel to use for profile; default = 1
finetuneCheck	[optional] 1 (default) - allow fine-tuning during the placing of measurements; 0 - instant placing
calcIntensity	[optional] 1 (default) - calculate intensity profile, 0 - do not calculate

Return values

calcIntensity result - 1-success, 0-cancel

Required fields of mibController:

Examples

obj.mibModel.I{obj.mibModel.Id}.hMeasure.PointFun(obj, [], 1); // call from mibMeasureToolController; place points and assign a label.

obj.mibModel.I{obj.mibModel.Id}.hMeasure.PointFun(obj, 2, 1); // call from mibMeasureToolController; edit second measurement.

References mibInputDlg(), mibController.mibModel, mibController.mibView, n, and mibController.plotImage().

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◆ removeMeasurements()

function mibMeasure.removeMeasurements ( index )

removeMeasurements(obj, index) Remove measurement(s) from the class

Parameters

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

Examples

obj.mibModel.I{obj.mibModel.I}.hMeasure.removeMeasurements(); // call from mibController;remove all measurements

obj.mibModel.I{obj.mibModel.I}.hMeasure.removeMeasurements(5); // call from mibController; remove 5th measurement

◆ setDefaultOptions()

function mibMeasure.setDefaultOptions ( )

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

Examples:

obj.mibModel.I{obj.mibModel.I}.hMeasure.setDefaultOptions(); // call from mibController;

◆ setOptions()

function mibMeasure.setOptions ( )

Update all values of the Options structure of the class.

Examples:

obj.mibModel.I{obj.mibModel.I}.hMeasure.setOptions(); call from mibController;

mibController

main controller for MIB

Definition mibController.m:18

References A(), and mibInputMultiDlg().

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◆ updateROIposition1()

function mibMeasure.updateROIposition1 ( new_position )

Update ROI position during movement of imrect and imellipse.

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

Parameters

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

References max.

◆ updateROIposition2()

function mibMeasure.updateROIposition2 ( new_position )

Update position during movement of impoly, imline.

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

Parameters

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

References max.

◆ updateROIScreenPosition()

function mibMeasure.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

obj.mibModel.I{obj.mibModel.I}.hMeasure.updateROIScreenPosition('crop'); // call from mibController; update positions of all ROIs during zoom in/out

obj.mibModel.I{obj.mibModel.I}.hMeasure.updateROIScreenPosition('full'); // call from mibController; update positions of all ROIs during panning

References max.

Member Data Documentation

◆ addMeasurement

EVENT mibMeasure.addMeasurement

add a new measurement, when the Measure Tool is displayed note: use this syntax instead to send event motifyEvent.Name = addMeasurement; eventdata = ToggleEventData(motifyEvent); notify(obj.mibModel, modelNotify, eventdata);

Events: addMeasurement

◆ Data

mibMeasure.Data

a structure with measurements .Data.n - index, double .Data.type - type, string: LinDistance, .Data.value - value, double .Data.info - info, free text .Data.X - X-coordinates of points .Data.Y - Y-coordinates of points .Data.Z - Z-coordinates of points .Data.T - T-coordinates of points .Data.orientation - orientation of the measurement: 4-yx; 1-zx; 2-zy .Data.spline .Data.circ .Data.intensity - average intensity of the profile .Data.profile - intensity profile .Data.integrateWidth - only for Distance (linear) width of the integrated intensity profile, otherwise empty

◆ fixZ

mibMeasure.fixZ

a switch that fixes Z and T values when the measurements are recalculated

◆ hImg

mibMeasure.hImg

handle to mibImage class

Referenced by mibMeasure().

◆ Options

mibMeasure.Options

a structure with show options .Options.marker1 = o; - style 1 for markers .Options.marker2 = .; - style 2 for markers .Options.markersize = 10; - size of markers .Options.linestyle1 = -; - style 1 for lines .Options.linestyle2 = –; - style 2 for lines .Options.linewidth = 1 ; - width for lines .Options.color1 = y; - color style 1 .Options.color2 = k; - color style 2 .Options.textcolorfg = y; - text color .Options.textcolorbg = none; - color for text background .Options.fontsize = 14; - size of the font .Options.splinemethod = spline; - method for splines .Options.showMarkers = 1; .Options.showLines = 1; .Options.showText = 1;

◆ roi

mibMeasure.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

◆ typeToShow

mibMeasure.typeToShow

a string that defines type of measurements to show:

All - show all
Angle
Caliper
Circle (R)
Distance (linear)
Distance (polyline)
Point

◆ updatePosition

EVENT mibMeasure.updatePosition

update coordinates of measurements

Events: updatePosition

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

Classes/@mibMeasure/mibMeasure.m

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ mibMeasure()

Member Function Documentation

◆ addMeasurements()

◆ addMeasurementsToPlot()

◆ AngleFun()

◆ CaliperFun()

◆ circlefit()

◆ CircleFun()

◆ clearContents()

◆ clearData()

◆ DistanceFreeFun()

◆ DistanceFun()

◆ DistancePolyFun()

◆ drawROI()

◆ editMeasurements()

◆ generateKymograph()

◆ getNumberOfMeasurements()

◆ PointFun()

◆ removeMeasurements()

◆ setDefaultOptions()

◆ setOptions()

◆ updateROIposition1()

◆ updateROIposition2()

◆ updateROIScreenPosition()

Member Data Documentation

◆ addMeasurement

◆ Data

◆ fixZ

◆ hImg

◆ Options

◆ roi

◆ typeToShow

◆ updatePosition