Labels Class Reference

class is responsible for keeping Labels/Annotations of the model More...

Inheritance diagram for Labels:

Collaboration diagram for Labels:

Public Member Functions
	Labels ()
	Constructor for the class.
function	clearContents ()
	Set all elements of the class to default values.
function	addLabels (labels, positions, values)
	Add labels with positions to the class.
function	crop (cropF)
	Recalculation of annotation positions during image crop.
function [ labelsList , labelValues , labelPositions , indices ] =	getCurrentSliceLabels ()
	[labelsList, labelValues, labelPositions, indices] = getCurrentSliceLabels(obj) Get list of labels shown at the current slice
function [ labelsList , labelValues , labelPositions , indices ] =	getLabels (rangeZ, rangeX, rangeY, rangeT)
	Get list of labels.
function [ labels , values , positions , indices ] =	getLabelsById (labelId)
	Get labels using labelId.
function labelsNumber =	getLabelsNumber ()
	Get total number of labels.
function [ labelsList , labelValues , labelPositions , indices ] =	getSliceLabels (handles, sliceNumber, timePoint)
	[labelsList, labelValues, labelPositions, indices] = getSliceLabels(obj, handles, sliceNumber, timePoint) Get list of labels shown at the specified slice
function [ minZ , labelIds ] =	getMinValueZ ()
	find and return the minimum Z value for all annotations as well as their indices
function [ maxZ , labelIds ] =	getMaxValueZ ()
	find and return the maximum Z value for all annotations as well as their indices
function	removeLabels (labels)
	removeLabels(obj, labels) Remove specified labels
function result =	renameLabels (oldLabel, newLabelText)
	Rename specified labels with new text.
function	replaceLabels (labels, positions, values)
	replaceLabels(obj, labels, positions, values) Replace existing labels with a new list of labels and their values
function result =	updateLabels (oldLabel, newLabelText, newLabelPos, newLabelValues)
	Update specified labels with newLabels.
function	saveToFile (filename, options)
	save Labels to a file
function	sortLabels (sortBy, direction)
	Resort the list of annotation labels.

Public Attributes
	labelText
	a cell array with labels
	labelValue
	an array with values for labels
	labelPosition
	a matrix with coordinates of the labels [pointIndex, z x y t]

Detailed Description

class is responsible for keeping Labels/Annotations of the model

Constructor & Destructor Documentation

Labels()

Labels.Labels

(

)

Constructor for the class.

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

Member Function Documentation

addLabels()

function Labels.addLabels	(		labels,
			positions,
			values )

Add labels with positions to the class.

Parameters

labels	a cell array with labels
positions	a matrix with coordinates of the labels [pointIndex, z x y t]
values	an array of numbers with values for the labels [optional], default = 1 Return values:

Examples:

labels{1} = 'my label 1';
labels{2} = 'my label 2';
positions(1,:) = [50, 75, 1, 3]; // position 1: z=1, x=50, y=75, t=3;            
positions(2,:) = [50, 75, 2, 5]; // position 1: z=2, x=50, y=75, t=5;

obj.mibModel.I{obj.mibModel.Id}.hLabels.addLabel(labels, positions); // add a labels to the list, call from mibController 

addLabel(obj, labels, positions); // Call within the class;  add a labels to the list 

clearContents()

function Labels.clearContents

(

)

Set all elements of the class to default values.

Examples:

obj.mibModel.I{obj.mibModel.Id}.hLabels.clearContents(); 

clearContents(obj); // Call within the class 

crop()

function Labels.crop

(

cropF

)

Recalculation of annotation positions during image crop.

Parameters

cropF

a vector [x1, y1, dx, dy, z1, dz, t1, dt] with parameters of the crop. Note! The units are pixels! Parameters t1 and dt are optional!

Examples:

cropF = [100 512 200 512 5 20 7 15];  // define parameters of the crop  

cropF2 = [100 512 NaN NaN 5 NaN 7 NaN];  // alternative definition of parameters for the crop  

obj.mibModel.I{obj.mibModel.Id}.hLabels.crop(cropF); // adjust coordinates due to cropping 

Attention

parameters dx, dy, dz, dt are not used, so they can be replaced with NaNs

getCurrentSliceLabels()

function [ labelsList , labelValues , labelPositions , indices ] = Labels.getCurrentSliceLabels

(

)

[labelsList, labelValues, labelPositions, indices] = getCurrentSliceLabels(obj) Get list of labels shown at the current slice

Note

replaced with mibImage.getSliceLabels

Return values

labelsList	a cell array with labels
labelPositions	a matrix with coordinates of the labels [labelIndex, z x y t]
indices	indices of the labels

Examples:

[labelsList, labelPositions, indices] = LabelsInstance.getCurrentSliceLabels(); // get all labels from the currently shown slice 

[labelsList, labelPositions, indices] = getCurrentSliceLabels(obj); // Call within the class;  get all labels from the currently shown slice 

Referenced by getSliceLabels().

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getLabels()

function [ labelsList , labelValues , labelPositions , indices ] = Labels.getLabels	(		rangeZ,
			rangeX,
			rangeY,
			rangeT )

Get list of labels.

Parameters

rangeZ	[optional] define range of labels to retrieve for Z [minZ maxZ], can be NaN
rangeX	[optional] define range of labels to retrieve for X [minX maxX], can be NaN
rangeY	[optional] define range of labels to retrieve for Y [minY maxY], can be NaN
rangeT	[optional] define range of labels to retrieve for T [minT maxT], can be NaN

Return values

labelsList	a cell array with labels
labelValues	an array of numbers with values
labelPositions	a matrix with coordinates of the labels [labelIndex, z x y t]
indices	indices of the labels

Examples:

[labelsList, labelValues, labelPositions, indices] = obj.mibModel.I{obj.mibModel.Id}.hLabels.getLabels(); // get all labels 

[labelsList, labelValues, labelPositions, indices] = obj.mibModel.I{obj.mibModel.Id}.hLabels.getLabels(50); // get all labels from slice 50 

[labelsList, labelValues, labelPositions, indices] = obj.mibModel.I{obj.mibModel.Id}.hLabels.getLabels(obj, 50); // Call within the class;  get all labels from slice 50 

getLabelsById()

function [ labels , values , positions , indices ] = Labels.getLabelsById

(

labelId

)

Get labels using labelId.

Parameters

labelId

a variable or a vector with an old label to be updated: a single number or a column of numbers: remove label that have index equal to the number a matrix: remove all labels that have coordinates specified in the matrix [labelIndex, z x y t] a cell array: remove all labels that have text specified in the cell array newLabelText, a cell or a char string with new text for the label

Return values

labels	- cell array with labels of annotations
values	- array with values of annotations
positions	- a matrix with coordinates (index; z,x,y,t)
indices	- array with indices of annoations | Examples: labelIds = [5, 7, 10]'; [labels, values, positions, id] = obj.mibModel.I{obj.mibModel.Id}.hLabels.getLabelsById(labelIds); // call from mibController, get labels with indices 5, 7, 10

getLabelsNumber()

function labelsNumber = Labels.getLabelsNumber

(

)

Get total number of labels.

Return values

labelsNumber

a number of labels

Examples:

labelsNumber = obj.mibModel.I{obj.mibModel.Id}.hLabels.getLabelsNumber(); // get number of labels 

labelsNumber = getLabelsNumber(obj); // Call within the class;  get number of labels  

getMaxValueZ()

function [ maxZ , labelIds ] = Labels.getMaxValueZ

(

)

find and return the maximum Z value for all annotations as well as their indices

Return values

maxZ	value of max Z for all annotations
labelIds	indices of those annotations

References max.

getMinValueZ()

function [ minZ , labelIds ] = Labels.getMinValueZ

(

)

find and return the minimum Z value for all annotations as well as their indices

Return values

minZ	value of min Z for all annotations
labelIds	indices of those annotations

References min.

getSliceLabels()

function [ labelsList , labelValues , labelPositions , indices ] = Labels.getSliceLabels	(		handles,
			sliceNumber,
			timePoint )

[labelsList, labelValues, labelPositions, indices] = getSliceLabels(obj, handles, sliceNumber, timePoint) Get list of labels shown at the specified slice

Parameters

handles	a handles structure of im_browser
sliceNumber	[optional], a slice number to get labels
timePoint	[optional], a time point to get the labels

Return values

labelsList	a cell array with labels
labelPositions	a matrix with coordinates of the labels [labelIndex, z x y]
indices	indices of the labels

Required fields of handles:

Examples:

[labelsList, labelPositions, indices] = obj.mibModel.I{obj.mibModel.Id}.hLabels.getSliceLabels(handles, 15); // get all labels from the slice 15 

[labelsList, labelPositions, indices] = getSliceLabels(obj, handles); // Call within the class;  get all labels from the currently shown slice 

References getCurrentSliceLabels().

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removeLabels()

function Labels.removeLabels

(

labels

)

removeLabels(obj, labels) Remove specified labels

Parameters

labels

a variable or a vector with a label: omitted: remove all labels a single number or a column of numbers: remove label that have index equal to the number a matrix: remove all labels that have coordinates specified in the matrix [labelIndex, z x y t] a cell array: remove all labels that have text specified in the cell array

Examples:

labels{1} = 'my label 1';

obj.mibModel.I{obj.mibModel.Id}.hLabels.removeLabels(labels); // remove annotations that match labels 

removeLabels(obj, labels); // Call within the class; remove annotations that match labels  

renameLabels()

function result = Labels.renameLabels	(		oldLabel,
			newLabelText )

Rename specified labels with new text.

Parameters

oldLabel	a variable or a vector with an old label to be updated: a single number or a column of numbers: remove label that have index equal to the number a matrix: remove all labels that have coordinates specified in the matrix [labelIndex, z x y t] a cell array: remove all labels that have text specified in the cell array
newLabelText	a cell or a char string with new text for the label

Return values

result

result of the function work: 1 - good, 0 - bad

Examples:

oldLabelId = [5, 7, 10]';
label{1} = 'my label 1';

obj.mibModel.I{obj.mibModel.Id}.hLabels.renameLabels(oldLabelId, label); // call from mibController, rename labels with indices 5, 7, 10 

replaceLabels()

function Labels.replaceLabels	(		labels,
			positions,
			values )

replaceLabels(obj, labels, positions, values) Replace existing labels with a new list of labels and their values

Parameters

labels	a cell array with labels
positions	a matrix with coordinates of the labels [pointIndex, z x y t]
values	an array of numbers with values of the labels, [optional] default = 1

Examples:

labels{1} = 'my label 1';
labels{2} = 'my label 2';
positions(1,:) = [1, 50, 75, 5]; // position 1: x=50, y=75, z=1,t=5;
positions(2,:) = [2, 50, 75, 6]; // position 1: x=50, y=75, z=2, t=6;

obj.mibModel.I{obj.mibModel.Id}.hLabels.replaceLabels(labels, positions); // replace labels with a new list 

replaceLabels(obj, labels, positions); // Call within the class; replace labels with a new list 

Referenced by mibAnnotationsController.loadBtn_Callback().

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saveToFile()

function Labels.saveToFile	(		filename,
			options )

save Labels to a file

Parameters

filename

full path to file

options

a structure with optional paramters .format - a char string ann - MIB annotation format landmarksAscii - amira landmarks in the ascii format landmarksBin - amira landmarks as binaries psi - PSI format ASCII xls - Microsoft Excel format .showWaitbar - [optional] a number 1-show; 0-do not show the waitbar .outputDir - [optional] output directory .convertToUnits - [optional] a logical, or not convert pixel coordinates to the units requires bounding box and pixSize information .boundingBox - a matrix [x1 width y1 height z1 depth], required for conversion to units .pixSize - a MIB structure with pixel sizes .labelText - [optional], instead of obj.labelText save provided labelText .labelPosition - [optional], instead of obj.labelPosition save provided labelPosition .labelValue - [optional], instead of obj.labelValue save provided labelValue .sliceNames - [optional], cell array with filenames, used for export to excel and csv .addLabelToFilename - [optional], logical add annotation label to filename, default = false

Required fields of options:

References labelPosition, labelText, labelValue, points2amiraLandmarks(), points2psi(), and xlswrite2().

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sortLabels()

function Labels.sortLabels	(		sortBy,
			direction )

Resort the list of annotation labels.

Parameters

sortBy	a string with the field to be used for sorting name, default sort by the label name value, sort by value x, sort by the X coordinate y, sort by the Y coordinate z, sort by the Z coordinate t, sort by the T coordinate
direction	a string with sorting direction ascend, default sort in the ascending order descend, sort in the descending order

Examples:

obj.mibModel.I{obj.mibModel.Id}.hLabels.sortLabels(); // call from mibController, sort the list by the label name 

obj.mibModel.I{obj.mibModel.Id}.hLabels.sortLabels('name', 'descend'); // call from mibController, sort the list by the label name using descending order 

updateLabels()

function result = Labels.updateLabels	(		oldLabel,
			newLabelText,
			newLabelPos,
			newLabelValues )

Update specified labels with newLabels.

Parameters

oldLabel	a variable or a vector with an old label to be updated: a single number or a column of numbers: remove label that have index equal to the number a matrix: remove all labels that have coordinates specified in the matrix [labelIndex, z x y t] a cell array: remove all labels that have text specified in the cell array
newLabelText	a cell or a char string with new text for the label
newLabelPos	coordinates of the new label [z, x, y]
newLabelValues	an array of numbers with values of the labels, [optional] default = 1

Return values

result

result of the function work: 1 - good, 0 - bad

Examples:

label{1} = 'my label 1';
newPosition(1,:) = [50, 75, 1, 5]; // position 1: x=50, y=75; z=1, t=5

obj.mibModel.I{obj.mibModel.Id}.hLabels.updateLabels(label, label, newPosition); // call from mibController, update coordinates of a label that has "my label 1" text 

Member Data Documentation

labelPosition

Labels.labelPosition

a matrix with coordinates of the labels [pointIndex, z x y t]

Referenced by saveToFile().

labelText

Labels.labelText

a cell array with labels

Referenced by saveToFile().

labelValue

Labels.labelValue

an array with values for labels

Referenced by saveToFile().

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

• Classes/@Labels/Labels.m