imageData Class Reference

class is resposnible to keep and visualize datasets More...

Inheritance diagram for imageData:

Collaboration diagram for imageData:

Public Member Functions
function handles =	addColorChannel (img, handles, channelId, lutColors)
	Add a new color channel to the existing dataset. More...
function	clearContents (handles)
	Set all elements of the class to default values. More...
function	clearMask (height, width, z, t)
	Clear the Mask layer. It is also possible to specify the area where the Mask layer should be cleared. More...
function [ handles , status ] =	convertImage (format, handles)
	Convert image to specified format: grayscale, truecolor, indexed and uint8, uint16, uint32 class. More...
function [ x , y , z , t ] =	convertMouseToDataCoordinates (x, y, mode, permuteSw)
	Convert coordinates under the mouse cursor to the coordinates of the dataset. More...
function [ x , y ] =	convertDataToMouseCoordinates (x, y, mode, magFactor)
	Convert coordinates of a pixel in the dataset to the coordinates of the imageView axes. More...
function	convertModel (type)
	Convert model from uint6 to uint8 and other way around. More...
function	copyColorChannel (channel1, channel2)
	Copy intensity from the first color channel (channel1) to the position of the second color channel (channel2). More...
function	createModel (model_type)
	Create an empty model: allocate memory for a new model. More...
function	cropDataset (cropF)
	Crop image and all corresponding layers of the opened dataset. More...
function	deleteColorChannel (channel1)
	Delete specified color channel from the dataset. More...
function result =	deleteSlice (sliceNumber, orient)
	Delete specified slice from the dataset. More...
function bb =	getBoundingBox ()
	Get Bounding box info as a vector [xmin, width, ymin, height, zmin, thickness]. More...
function slice =	getCurrentSlice (type, countour_id)
	Get currently shown slice. More...
function slice_no =	getCurrentSliceNumber ()
	Get slice number of the currently shown image. More...
function timePnt =	getCurrentTimePoint ()
	Get time point of the currently shown image. More...
function slice =	getData2D (type, slice_no, orient, col_channel, custom_img, options)
	Get the 3D slice: height:width:colors. More...
function dataset =	getData3D (type, time, orient, col_channel, options, custom_img)
	Get the 4D dataset: height:width:colors:depth. More...
function dataset =	getData4D (type, orient, col_channel, options, custom_img)
	Get complete 4D dataset. More...
function dataset =	getDataset (type, permuteSw, col_channel, options)
	Get 4D dataset, [height, width, color, depth], LEGACY function, please use imageData.getData3D instead! More...
function imgRGB =	getRGBimage (handles, options, sImgIn)
	Generate RGB image from all layers that have to be shown on the screen. More...
function	invertColorChannel (channel1)
	Invert color channel of the dataset. More...
function	generateModelColors ()
	Generate list of colors for materials of a model. More...
function [ height , width , color , thick , time ] =	getDatasetDimensions (type, orient, color, options)
	Get dimensions of the dataset. More...
function slice =	getFullSlice (type, slice_no, orient, col_channel, custom_img, options)
	Get the whole, uncropped 3D slice. More...
function [ totalSize , imSize ] =	getDatasetSizeInBytes ()
	Get size of the loaded dataset in bytes. More...
function modelMaterialNames =	getMaterialNames ()
	Get names of materials of the model. More...
function imgOut =	getRoiCrop (type, handles, roiNo, options, col_channel)
	Get a 3D dataset from the defined ROI regions. More...
function imgOut =	getRoiCropSlice (type, handles, roiNo, sliceNo, orient, options, col_channel)
	Get a 2D slice of the ROI regions only. More...
function [ yMin , yMax , xMin , xMax ] =	getCoordinatesOfShownImage ()
	Return minimal and maximal coordinates (XY) of the image that is currently shown. More...
function slice =	getSlice (type, slice_no, orient, col_channel, custom_img, options)
	Get the 2D slice. More...
function slice =	getSliceToShow (type, slice_no, orient, col_channel, custom_img, options)
	Get a part of the 3D slice that fits into the viewing window of the handles.imageAxes, Note! the image will be cropped. More...
function	insertEmptyColorChannel (channel1)
	Insert an empty color channel to the specified position. More...
function handles =	insertSlice (img, handles, insertPosition, img_info)
	Insert a slice or a dataset into the existing volume. More...
function	mark2selection (layer_id, type, str_type, xy_vec)
	Add a marker/pointer to the selection layer. More...
function	moveMaskToSelectionDataset (action_type, options)
	Move the Mask layer to the Selection layer. More...
function	moveModelToMaskDataset (action_type, options)
	Move the selected Material to the Mask layer. More...
function	moveModelToSelectionDataset (action_type, options)
	Move the selected Material to the Selection layer. More...
function	moveSelectionToMaskDataset (action_type, options)
	Move the Selection layer to the Mask layer. More...
function	moveSelectionToModelDataset (action_type, options)
	Move selection layer to the model layer. More...
function	moveView (x, y, orient)
	Center the image view at the provided coordinates: x, y. More...
function handles =	plotImage (axes, handles, resize, sImgIn)
	Plot image to the axes. The main drawing function. More...
function handles =	replaceDataset (img, handles, img_info, modelImg, maskImg, selectionImg)
	Replace existing dataset with a new one. More...
function handles =	replaceImageColor (handles, type)
	Replace image intensities in the Masked or Selected areas with new intensity value. More...
function	resizeImage (new_width, new_height, method)
	Resize all layers using specified method. More...
function	rotateColorChannel (channel1)
	Rotate color channel of the dataset. More...
function	clearSelection (height, width, z, t)
	Clear the Selection layer. It is also possible to specify the area where the Selection layer should be cleared. More...
function	setCurrentSlice (type, slice, color_id)
	Update the currently shown slice of the dataset. More...
function result =	setData2D (type, slice, slice_no, orient, col_channel, custom_img, options)
	set the 3D slice: height:width:colors to the dataset More...
function result =	setData3D (type, dataset, time, orient, col_channel, options, custom_img)
	Set the 4D dataset (height:width:colors:depth) into the 5D dataset. More...
function result =	setData4D (type, dataset, orient, col_channel, options)
	result = setData4D(obj, type, dataset, orient, col_channel, options) Set complete 5D dataset More...
function result =	setDataset (type, dataset, permuteSw, col_channel, options)
	Update complete 4D dataset, LEGACY function, please use imageData.setData3D instead! More...
function custom_img =	setFullSlice (type, slice, slice_no, orient, col_channel, custom_img, options)
	Update the full 2D slice of the dataset. More...
function handles =	setMaterialNames (modelMaterialNames, handles)
	Set names for materials of the model. More...
function	setRoiCrop (type, imgIn, handles, roiNo, options, col_channel)
	Update a full 3D dataset from the defined ROI regions. More...
function	setRoiCropSlice (type, imgIn, handles, roiNo, sliceNo, orient, options, col_channel)
	Update a 2D slice of the ROI regions of the dataset. More...
function custom_img =	setSlice (type, slice, slice_no, orient, col_channel, custom_img, options)
	Update the 2D slice of the dataset. More...
function custom_img =	setSliceToShow (type, slice, slice_no, orient, col_channel, custom_img, options)
	Update the croped to the viewing window 2D slice of the dataset. More...
function	swapColorChannels (channel1, channel2)
	Swap two color channels of the dataset. More...
function	transpose (new_orient)
	Change orientation of the image to the XY, XZ, or YZ plane. More...
function handles =	updateAxesLimits (handles, mode, newMagFactor)
	Updates the imageData.axesX and imageData.axesY during fit screen, resize, or new dataset drawing. More...
function	updateBoundingBox (newBB, xyzShift, imgDims)
	Update the bounding box info of the dataset. More...
function	updateDisplayParameters ()
	Update display parameters for visualization. More...
function	updateImgInfo (addText, action, entryIndex)
	Update action log. More...
function result =	updateParameters (pixSize)
	Update imageData.pixelSize, imageData.img_info('XResolution') and imageData.img_info('XResolution') More...
	imageData (handles, model_type, img)
	Constructor for the imageData class. More...

Public Attributes
	axesX
	a vector [min, max] with minimal and maximal coordinates of the axes X of the imageAxes axes More...
	axesY
	a vector [min max] with minimal and maximal coordinates of the axes Y of the imageAxes axes More...
	blockModeSwitch
	defines whether to get the whole dataset or only the shown part of it, either 0 or 1 More...
	brush_prev_xy
	coordinates of the previous pixel for the Brush tool, More...
	brush_selection
	selection layer during the brush tool movement, More...
	colors
	number of color channels More...
	current_yxz
	a vector to remember last selected slice number of each yx, zx, zy planes, More...
	height
	image height, px More...
	hLabels
	a handle to class to keep labels More...
	hMeasure
	a handle to class to keep measurements More...
	hROI
	handle to ROI class, roiImage More...
	img
	a property to keep the Image layer. More...
	img_info
	information about the dataset, an instance of the containers.Map class Default keys: More...
	imh
	handle for the currently shown image More...
	Ishown
	a property to keep the currently displayed image in RGB format More...
	lutColors
	a matrix with LUT colors [1:colorChannel, R G B], (0-1) More...
	magFactor
	magnification factor for the currently shown image, 1=100%, 1.5 = 150% More...
	maskExist
	a switch to indicate presense of the Mask layer. Can be 0 (no model) or 1 (model exist) More...
	maskImg
	a property to keep the Mask layer More...
	maskImgFilename
	file name of the Mask layer image More...
	maskStat
	Statistics for the Mask layer with the PixelList info returned by regionprops Matlab function. More...
	model
	model is a property to keep the Model layer More...
	model_fn
	model_fn is a property to keep filename of the Model layer More...
	model_type
	The type of a model. More...
	model_var
	model_var is a variable name in the mat-file to keep the Model layer More...
	model_diff_max
	maximal absolute value in the image model of the diff_map type More...
	modelMaterialColors
	a matrix of colors [0-1] for materials of the Model, [materialIndex, R G B] More...
	modelMaterialNames
	an array of strings to define names of materials of the Model More...
	modelExist
	a switch to indicate presense of the Model layer. Can be 0 (no model) or 1 (model exist) More...
	no_stacks
	number of stacks in the dataset More...
	orientation
	Orientation of the currently shown dataset,. More...
	pixSize
	a structure with diminsions of voxels, More...
	selection
	a property to keep the Selection layer More...
	slices
	coordinates of the shown slice borders More...
	storedSelection
	a buffer to store selection with press of Ctrl+C button, and restore with Ctrl+V More...
	time
	number of time points in the dataset More...
	trackerYXZ
	starting point for the Membrane Click-tracer tool More...
	viewPort
	a structure More...
	volren
	a structure with parameters for the volume rendering the fields are More...
	width
	image width, px More...
EVENT	none
	Description of events when selected two or more curves More...

Detailed Description

class is resposnible to keep and visualize datasets

Constructor & Destructor Documentation

imageData.imageData	(		handles,
			model_type,
			img
	)

Constructor for the imageData class.

Create a new instance of the class with default parameters.

Parameters

handles

- [optional] handles structure of im_browser model_type - [optional], parameter to setup the model type img - [optional], image to use to initialize imageData class

Required fields of handles:

References model_type.

Member Function Documentation

function handles = imageData.addColorChannel	(		img,
			handles,
			channelId,
			lutColors
	)

Add a new color channel to the existing dataset.

Parameters

img	new 2D/3D image stack to add
handles	handles structure from im_browser
channelId	[optional] number (single!) of the channel to add, if NaN a new color channel is created
lutColors	[optional] a matrix (channelNumber, R G B) for the colors. The colors should be in range between 0 and 1

Return values

handles

handles structure from im_browser

Example:

handles = imageData.addColorChannel(img, handles, channelId);     // replace the color channel (channelId) with new img  

handles = addColorChannel(obj, img); // Call within the class; add img as a new color channel 

References img, and lutColors.

function imageData.clearContents

(

img

)

Set all elements of the class to default values.

Parameters

img	- [optional], image to use to initialize imageData class

Examples:

imageData.clearContents(); 

clearContents(obj); // Call within the class 

References img, and makeViewMatrix().

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function imageData.clearMask	(		height,
			width,
			z,
			t
	)

Clear the Mask layer. It is also possible to specify the area where the Mask layer should be cleared.

Parameters

height	[optional] vector of heights, for example [1:imageData.height] or 0 - to initialize space for the new Mask
width	[optional] vector of width, for example [1:imageData.width]
z	[optional] vector of z-values, for example [1:imageData.no_stacks]
t	[optional] vector of t-values, for example [1:imageData.time]

Examples:

imageData.clearMask();  // clear the mask layer 

clearMask(obj);   // Call within the class; clear the mask layer 

function imageData.clearSelection	(		height,
			width,
			z,
			t
	)

Clear the Selection layer. It is also possible to specify the area where the Selection layer should be cleared.

Parameters

height	[optional], can be NaN, a vector of heights(for example [1:imageData.height]) or a string with the mode (2D, 3D, 4D)
width	[optional], can be NaN, a vector of width, for example [1:imageData.width]
z	[optional] a vector of z-values, for example [1:imageData.no_stacks]
t	[optional] a vector of t-values, for example [1:imageData.time]

Examples:

imageData.clearSelection(); // Clear the Selection layer completely 

imageData.clearSelection(1:imageData.height, 1:imageData.width, 1:3); // Clear the Selection layer only in 3 first slices  

clearSelection(obj);  // Call within the class to clear the Selection layer completely 

References height, img, and width.

function [ xOut , yOut ] = imageData.convertDataToMouseCoordinates	(		x,
			y,
			mode,
			magFactor
	)

Convert coordinates of a pixel in the dataset to the coordinates of the imageView axes.

Parameters

x	x - coordinate
y	y - coordinate
mode	a string that defines a mode of the shown image: shown (in most cases), or full (for panning)
magFactor	[optional], used to force magFactor, default obj.magFactor

Return values

xOut	x - coordinate with the dataset
yOut	y - coordinate with the dataset

Examples:

[xOut,yOut] = imageData.convertDataToMouseCoordinates(x, y);  // do conversion' 

[xOut,yOut] = convertDataToMouseCoordinates(obj,x, y);   // Call within the class; do conversion 

function [ handles , status ] = imageData.convertImage	(		format,
			handles
	)

Convert image to specified format: grayscale, truecolor, indexed and uint8, uint16, uint32 class.

Parameters

format

description of the new image format 'grayscale' - grayscale image, 1 color channel 'truecolor' - truecolor image, 2 or 3 color channels (red, green, blue) 'hsvcolor' - hsv color image, 3 color channels (hue, saturation, value) 'indexed' - indexed colors, the color map is stored in imageData.img_info. Colormap 'uint8' - 8-bit unsinged integer, [0 - 255] levels 'uint16' - 16-bit unsinged integer, [0 - 65535] levels; 'uint32' - 32-bit unsinged integer, [0 - 4294967295] levels; Note! Not Really tested...

handles

handles of im_browser.m

Return values

handles	handles of im_browser.m
status	1 -success, 0 -fail

Required fields of handles:

Examples:

handles = imageData.convertImage(handles, 'uint8');  // convert dataset to the uint8 class 

[handles, status] = convertImage(obj, handles, 'grayscale');   // Call within the class; convert dataset to the grayscale type 

References img, mib_inputdlg(), and updateGuiWidgets().

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function imageData.convertModel

(

type

)

Convert model from uint6 to uint8 and other way around.

Note

The current type is defined with imageData.model_type

Parameters

type	[optional] a type of a new model: uint8 or uint6

Examples:

imageData.convertModel('uint8');  // convert model to the uint8 type 

convertModel(obj, 'uint8');   // Call within the class; convert model to the uint8 type 

function [ xOut , yOut , zOut , tOut ] = imageData.convertMouseToDataCoordinates	(		x,
			y,
			mode,
			permuteSw
	)

Convert coordinates under the mouse cursor to the coordinates of the dataset.

Parameters

x	x - coordinate
y	y - coordinate
mode	[optional] a string that defines a mode of the shown image, default is shown shown - the most common one, convert coordinates of the mouse above the image to the coordinates of the dataset full - suppose to do the conversion for the situation when the full image is rendered in the handles.imageAxes, never used...? blockmode - when the blockface mode is switched on the function returns coordinates under the mouse for the Block
permuteSw	[optional], can be empty when 0 returns the coordinates for the dataset in the original xy-orientation; when 1 (default) returns coordinates for the dataset so that the currently selected orientation becomes xy

Return values

xOut	x - coordinate with the dataset
yOut	y - coordinate with the dataset
zOut	z - coordinate with the dataset
tOut	t - time coordinate

Examples:

[xOut,yOut] = imageData.convertMouseToDataCoordinates(x, y);  // do conversion' 

[xOut,yOut] = convertMouseToDataCoordinates(obj,x, y);   // Call within the class; do conversion 

function imageData.copyColorChannel	(		channel1,
			channel2
	)

Copy intensity from the first color channel (channel1) to the position of the second color channel (channel2).

The first color channel will be copied to the position of the second color channel

Parameters

channel1	[optional] index of the first color channel
channel2	[optional] index of the second color channel

Examples:

handles = imageData.copyColorChannel(1, 3);     // copy intensities from channel 1 to channel 3 

handles = copyColorChannel(obj, 1, 3); // Call within the class; copy intensities from channel 1 to channel 3 

References updateImgInfo().

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function imageData.createModel

(

model_type

)

Create an empty model: allocate memory for a new model.

Reinitialize imageData.model variable (NaN when no model present) with an empty matrix [imageData.height, imageData.width, imageData.no_stacks] of the defined type class

Parameters

model_type

type of the model, uint6 - a segmentation model with up to 63 materials; the Model, Mask and Selection layers stored in the same matrix, to decrease memory consumption; uint8 - a segmentation model with up to 255 materials; the Model, Mask and Selection layers stored in separate matrices; int8 - a model layer that has intensities from -128 to 128.%

Examples:

imageData.createModel('uint6');  // allocate space for a new Model layer, type 'uint6' 

createModel(obj,'uint6');   // Call within the class; allocate space for a new Model layer, type 'uint6 

References model_type.

function imageData.cropDataset

(

cropF

)

Crop image and all corresponding layers of the opened dataset.

Parameters

cropF

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

Examples:

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

imageData.cropDataset(cropF);  // do the crop 

cropDataset(obj, cropF);   // Call within the class; do the crop 

function imageData.deleteColorChannel

(

channel1

)

Delete specified color channel from the dataset.

Parameters

channel1

[optional] the index of color channel to delete.

Examples:

imageData.deleteColorChannel(3);     // delete color channel 3 from the obj.img 

deleteColorChannel(obj, 1); // Call within the class; delete color channel 1 from the obj.img 

References mib_inputdlg(), and updateImgInfo().

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function result = imageData.deleteSlice	(		sliceNumber,
			orient
	)

Delete specified slice from the dataset.

Parameters

sliceNumber

the number of the slice to delete

orient

[optional], can be NaN (in this case removes the currently shown) when 0 (default) remove slice from the current orientation (obj.orientation) when 1 remove slice from the zx configuration: [x,z,c,y,t] -> [y,x,c,z,t] when 2 remove slice from the zy configuration: [y,z,c,y,t] -> [y,x,c,z,t] when 3 not used when 4 remove slice from the yx configuration: [y,x,c,z,t] when 5 remove slice from the t configuration

Return values

result

result of the function, 0 fail, 1 success

Examples:

imageData.deleteSlice(3);     // delete the 3rd slice from the dataset 

deleteSlice(obj, 3); // Call within the class; delete the 3rd slice from the dataset 

function imageData.generateModelColors

(

)

Generate list of colors for materials of a model.

When a new material is added to a model, this function generates a random color for it.

Examples:

imageData.generateModelColors();  // generate colors 

generateModelColors(obj);   // Call within the class; generate colors 

function bb = imageData.getBoundingBox

(

)

Get Bounding box info as a vector [xmin, width, ymin, height, zmin, thickness].

The bounding box info is needed to properly put the dataset in the 3D space. It is stored in the header of the Amira mesh file, or in the beginning of the ImageDescription field of the TIF file.

Return values

bb	- bounding box info bb(1) = Xmin bb(2) = Width bb(3) = Ymin bb(4) = Height bb(5) = Zmin bb(6) = Thickness

Examples:

bb = imageData.getBoundingBox();  // get bounding box info 

bb = getBoundingBox(obj);   // Call within the class; get bounding box info 

function [ yMin , yMax , xMin , xMax ] = imageData.getCoordinatesOfShownImage

(

)

Return minimal and maximal coordinates (XY) of the image that is currently shown.

Return values

yMin	- minimal Y coordinate
yMax	- maximal Y coordinate
xMin	- minimal Y coordinate
xMax	- maximal Y coordinate

Examples:

[yMin, yMax, xMin, xMax] = imageData.getCoordinatesOfShownImage();  // get coordinates 

[yMin, yMax, xMin, xMax] = getCoordinatesOfShownImage(obj);   // Call within the class; get coordinates  

function slice = imageData.getCurrentSlice	(		type,
			countour_id
	)

Get currently shown slice.

Parameters

type	a string with type of the dataset to retrieve, image, model, mask, selection
countour_id	- [optional], when type is image, countour_id is a vector with color numbers to take, otherwise will take the colors selected in the imageData.slices{3} variable when type is model countour_id may be NaN - to take all material of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.

Return values

slice

3D image with dimensions [1:height, 1:width, 1:color]

Examples

slice = handles.Img{handles.Id}.I.getCurrentSlice('image');      // take the currently shown image  

slice = handles.Img{handles.Id}.I.getCurrentSlice('model', 4); // Get object 4 from the model 

slice = obj.getCurrentSlice('image');      // Call within the class 

Attention

sensitive to the imageData.blockModeSwitch

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getSlice.m wrapper function, as

slice = ib_getSlice('image', handles) 

function slice_no = imageData.getCurrentSliceNumber

(

)

Get slice number of the currently shown image.

Return values

slice_no

index of the currently shown slice

Examples:

slice_no = imageData.getCurrentSliceNumber();      // take the currently shown image  

slice_no = getCurrentSliceNumber(obj);      // Call within the class 

function timePnt = imageData.getCurrentTimePoint

(

)

Get time point of the currently shown image.

Return values

timePnt

index of the currently shown slice

Examples:

timePnt = imageData.getCurrentTimePoint();      // get the time point  

timePnt = getCurrentTimePoint(obj);      // Call within the class, get the time point 

function slice = imageData.getData2D	(		type,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

Get the 3D slice: height:width:colors.

Parameters

type	type of the slice to retrieve, image, model,mask, selection, custom (custom indicates to use custom_img as the dataset), everything(model,mask and selection for imageData.model_type=='uint6' only)
slice_no	[optional], an index of the slice to show, when NaN will show the current slice
orient	[optional], can be NaN when 0 (default) updates the dataset transposed from the current orientation (obj.orientation) when 1 returns transposed dataset from the zx configuration: [x,z,c,y,t] -> [y,x,c,z,t] when 2 returns transposed dataset from the zy configuration: [y,z,c,y,t] -> [y,x,c,z,t] when 3 not used when 4 returns original dataset from the yx configuration: [y,x,c,z,t] when 5 not used
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.
custom_img	[optional], can be NaN; the function return a slice not from the imageData class but from this custom_img, requires to specify the custom type. custom_img should be a 3D dataset.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - return full dataset, 1 - return only the shown part) .y -> [optional], [ymin, ymax] of the part of the slice to take .x -> [optional], [xmin, xmax] of the part of the slice to take .t -> [optional], [tmin, tmax] indicate the time point to take, when missing return the currently selected time point

Return values

slice

3D image. For the image type: [1:height, 1:width, 1:colors]; for all other types: [1:height, 1:width]

Required fields of options:

Examples:

slice = handles.Img{handles.Id}.I.getData2D('image', 5);      // get the 5-th slice of the current stack orientation  

slice = handles.Img{handles.Id}.I.getData2D('image', 5, 4, 2); // get the 5-th slice of the XY-orientation, color channel=2 

slice = handles.Img{handles.Id}.I.getData2D('custom', 5, 1, 2, custom_img); // get the 5-th slice of the YZ-orientation, color channel=2 from the custom_image 

slice = obj.getData2D(img, 'image', 5);      // Call within the class; get the 5-th slice of the current stack orientation  

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getSlice.m wrapper function, as

slice = ib_getSlice('image', handles); 

function dataset = imageData.getData3D	(		type,
			time,
			orient,
			col_channel,
			options,
			custom_img
	)

Get the 4D dataset: height:width:colors:depth.

Parameters

type	type of the slice to retrieve, image, model,mask, selection, custom (custom indicates to use custom_img as the dataset), everything(model,mask and selection for imageData.model_type=='uint6' only)
time	[optional], an index of the time point to show, when NaN gets the dataset for the current time point
orient	[optional], can be NaN when 0 (default) returns the dataset transposed to the current orientation (obj.orientation) when 1 returns transposed dataset to the zx configuration: [y,x,c,z] -> [x,z,c,y] when 2 returns transposed dataset to the zy configuration: [y,x,c,z] -> [y,z,c,y] when 3 not used when 4 returns original dataset to the yx configuration: [y,x,c,z] when 5 not used
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - return full dataset, 1 - return only the shown part) .y -> [optional], [ymin, ymax] of the part of the dataset to take .x -> [optional], [xmin, xmax] of the part of the dataset to take .z -> [optional], [zmin, zmax] of the part of the dataset to take
custom_img	[optional], can be NaN; the function return a slice not from the imageData class but from this custom_img, requires to specify the custom type. custom_img should be a 3D dataset.

Return values

dataset

4D image. For the image type: [1:height, 1:width, 1:colors, 1:depth]; for all other types: [1:height, 1:width, 1:depth]

Examples:

dataset = handles.Img{handles.Id}.I.getData3D('image');      // get the 4D dataset for the current time point, in the shown orientation  

dataset = handles.Img{handles.Id}.I..getData3D('image', 5, 4, 2); // get the 4D dataset for the 5-th time point in the XY orientation 

dataset = handles.Img{handles.Id}.I..getData3D('selection', 5, 1, 2, custom_img); // get the 5-th timepoint in the the XZ-orientation, color channel=2 

dataset = obj.getData3D(img, 'image', [], 4);      // Call within the class; get the 4D dataset for the current time point in the XY orientation  

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getDataset.m wrapper function, as

dataset = ib_getDataset('image', handles); 

function dataset = imageData.getData4D	(		type,
			orient,
			col_channel,
			options,
			custom_img
	)

Get complete 4D dataset.

Parameters

type	type of the dataset to retrieve, image, model,mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
orient	[optional], can be NaN when 0 (default) returns the dataset transposed to the current orientation (obj.orientation) when 1 returns transposed dataset to the zx configuration: [y,x,c,z,t] -> [x,z,c,y,t] when 2 returns transposed dataset to the zy configuration: [y,x,c,z,t] -> [y,z,c,y,t] when 3 not used when 4 returns original dataset to the yx configuration: [y,x,c,z,t] when 5 not used
col_channel	[optional], when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material will have index = 1.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - return full dataset, 1 - return only the shown part) .y -> [optional], [ymin, ymax] coordinates of the dataset to take after transpose, height .x -> [optional], [xmin, xmax] coordinates of the dataset to take after transpose, width .z -> [optional], [zmin, zmax] coordinates of the dataset to take after transpose, depth .t -> [optional], [tmin, tmax] coordinates of the dataset to take after transpose, time

Return values

dataset

4D or 5D stack. For the image type: [1:height, 1:width, 1:colors, 1:depth, 1:time]; for all other types: [1:height, 1:width, 1:thickness, 1:time]

Required fields of options:

Examples:

dataset = handles.Img{handles.Id}.I.getData4D('image');      // get the complete dataset in the shown orientation 

dataset = handles.Img{handles.Id}.I.getData4D('image', NaN, NaN, options.blockModeSwitch=1); // get the croped to the viewing window dataset, with shown colors 

dataset = handles.Img{handles.Id}.I.getData4D('image', 4, 2); // get complete dataset in the XY orientation with only second color channel 

dataset = obj.getData4D('image');      // Call within the class, get the complete dataset  

Attention

sensitive to the imageData.blockModeSwitch

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getDataset.m wrapper function, as

dataset = ib_getDataset('image', handles); 

function dataset = imageData.getDataset	(		type,
			orient,
			col_channel,
			options
	)

Get 4D dataset, [height, width, color, depth], LEGACY function, please use imageData.getData3D instead!

Parameters

type	type of the dataset to retrieve, image, model,mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
orient	[optional], can be NaN or empty when 0 (default) returns the dataset transposed to the current orientation (obj.orientation) when 1 returns transposed dataset to the zx configuration: [y,x,c,z] -> [x,z,c,y] when 2 returns transposed dataset to the zy configuration: [y,x,c,z] -> [y,z,c,y] when 3 not used when 4 returns original dataset to the yx configuration: [y,x,c,z] when 5 not used
col_channel	[optional], when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material will have index = 1.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - return full dataset, 1 - return only the shown part) .y -> [optional], [ymin, ymax] of the part of the dataset to take .x -> [optional], [xmin, xmax] of the part of the dataset to take .z -> [optional], [zmin, zmax] of the part of the dataset to take

Return values

dataset

4D stack. For the image type: [1:height, 1:width, 1:colors, 1:thickness]; for all other types: [1:height, 1:width, 1:thickness]

Examples:

dataset = handles.Img{handles.Id}.I.getDataset('image');      // get the complete 4D dataset in the shown orientation  

dataset = handles.Img{handles.Id}.I.getDataset('image', 0, NaN, options.blockModeSwitch=1); // get the croped to the viewing window dataset, with the shown colors 

dataset = handles.Img{handles.Id}.I.getDataset('image', 4, 2); // get transposed to the XY orientation dataset with only second color channel 

dataset = obj.getDataset('image');      // Call within the class, get the complete dataset  

Attention

sensitive to the imageData.blockModeSwitch

not sensitive to the shown ROI

legacy function, use imageData.getData3D insead!

for normal calls it is recommended to use ib_getDataset.m wrapper function, as

dataset = ib_getDataset('image', handles); 

References time.

function [ height , width , color , depth , time ] = imageData.getDatasetDimensions	(		type,
			orient,
			color,
			options
	)

Get dimensions of the dataset.

Parameters

type	type of the dataset to retrieve dimensions, image (default), model, mask, selection
orient	[optional], can be NaN when 0 (default) returns the dataset transposed to the current orientation (obj.orientation) when 1 returns dimensions of the transposed dataset to the zx configuration: [y,x,c,z,t] -> [x,z,c,y,t] when 2 returns dimensions of the transposed dataset to the zy configuration: [y,x,c,z,t] -> [y,z,c,y,t] when 3 not used when 4 returns dimensions of the original dataset to the yx configuration: [y,x,c,z,t] when 5 not used
color	[optional], can be NaN when type is image, color is a vector with color numbers to take, otherwise take the colors selected in the imageData.slices{3} variable when type is model color may be 0 - to take all materials of the model or an integer to take specific material.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - return dimensions of the full dataset, 1 - return dimensions of the shown part only) .orientation -> override the imageData.orientation parameter

Return values

height	height of the dataset
width	width of the dataset
color	vector of colors of the dataset
depth	number of z-layers of the dataset
time	number of time points

Required fields of options:

Examples:

[height width color depth] = imageData.getDatasetDimensions('image')      // get dimensions of the complete dataset  

[height width color depth] = imageData.getDatasetDimensions('image', 1);  // get dimensions of the transposed dataset  

[height width color depth] = getDatasetDimensions(obj, 'image', NaN, NaN, options.blockModeSwitch=1)      // Call within the class; get dimensions of the cropped not transposed, with shown colors dataset  

Attention

sensitive to the imageData.blockModeSwitch

not sensitive to the shown ROI

References height, time, and width.

function [ totalSize , imSize ] = imageData.getDatasetSizeInBytes

(

)

Get size of the loaded dataset in bytes.

For checking memory requirements when working with some functions (only for windows!). The amounts of physical memory used by Matlab and total memory available on the computer can be obtained with the following code

[userview, systemview] = memory;
systemview.PhysicalMemory.Available // total memory
userview.MemUsedMATLAB              // memory used by Matlab

Return values

totalSize	- total size of all layers in bytes
imSize	- size of the image layer in bytes

Examples:

[totalSize, imSize] = imageData.getDatasetSizeInBytes();  // get both total and matlab memory amounts 

[totalSize, imSize] = getDatasetSizeInBytes(obj);   // Call within the class; get both total and matlab memory amounts  

function slice = imageData.getFullSlice	(		type,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

Get the whole, uncropped 3D slice.

Parameters

type	type of the slice to retrieve, image, model,mask, selection, custom (custom indicates to use custom_img as the dataset), everything(model,mask and selection for imageData.model_type=='uint6' only)
slice_no	[optional], an index of the slice to show, when NaN show the current slice
orient	[optional], can be NaN when 0 (default) returns the dataset transposed to the current orientation (obj.orientation) when 1 returns transposed dataset to the zx configuration: [y,x,c,z,t] -> [x,z,c,y,t] when 2 returns transposed dataset to the zy configuration: [y,x,c,z,t] -> [y,z,c,y,t] when 3 not used when 4 returns original dataset to the yx configuration: [y,x,c,z,t] when 5 not used
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.
custom_img	the function return a slice not from the imageData class but from this custom_img, requires to specify the custom type. custom_img should be a 3D dataset.
options	[optional], a structure with extra parameters .y -> [optional], [ymin, ymax] of the part of the slice to take .x -> [optional], [xmin, xmax] of the part of the slice to take .t -> [optional], [tmin, tmax] the time point of the dataset; default is the currently shown time point

Return values

slice

2D image. For the image type: [1:height, 1:width, 1:colors]; for all other types: [1:height, 1:width]

Required fields of options:

Examples:

slice = handles.Img{handles.Id}.I.getFullSlice('image', 5);      // get the 5-th slice of the current stack orientation  

slice = handles.Img{handles.Id}.I.getFullSlice('image', 5, 4, 2); // get the 5-th slice of the XY-orientation, color channel=2 

slice = handles.Img{handles.Id}.I.getFullSlice('custom', 5, 1, 2, custom_img); // get the 5-th slice of the YZ-orientation, color channel=2 from the custom_image 

slice = obj.getFullSlice('image', 5, NaN, 2); // Call within the class; get the 5-th slice of the current orientation, color channel=2 from the custom_image 

Attention

not sensitive to the imageData.blockModeSwitch

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getSlice.m wrapper function, as

slice = ib_getSlice('image', handles, NaN, NaN, NaN, options.blockModeSwitch=0); 

References height, and width.

function modelMaterialNames = imageData.getMaterialNames

(

)

Get names of materials of the model.

Return values

modelMaterialNames

a cell array with names of materials

Example:

modelMaterialNames = imageData.getMaterialNames();     // get list of materials  

modelMaterialNames = getMaterialNames(obj); // Call within the class; get list of materials 

References modelMaterialNames.

function imgRGB = imageData.getRGBimage	(		handles,
			options,
			sImgIn
	)

Generate RGB image from all layers that have to be shown on the screen.

| Examples

options.mode = 'shown'; 

imageData.Ishown = imageData.getRGBimage(handles, options);     // to get cropped 2D RGB image of the shown area 

imageData.Ishown = getRGBimage(obj, handles, options);// Call within the class; to get cropped 2D RGB image of the shown area 

Parameters

handles	handles structure from im_browser
options	a structure with extra parameters: .mode -> full -> return RGB image of the whole slice; shown -> return RGB image of the shown area only .resize -> yes -> resize RGB image to the current magnification value [default]; no -> return the image in the original resolution .sliceNo [optional] -> index of a slice to show .markerType [optional] -> default NaN, type of annotations: when both show a label next to the position marker, when marker - show only the marker without the label, when text - show only text without marker .t -> [optional], [tmin, tmax] the time point of the dataset; default is the currently shown time point
sImgIn	a custom 3D stack to grab a single 2D slice from

Return values

imgRGB

- RGB image with combined layers, [1:height, 1:width, 1:3]

Required fields of options:

Required fields of handles:

References ib_addText2Img().

Referenced by plotImage().

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function imgOut = imageData.getRoiCrop	(		type,
			handles,
			roiNo,
			options,
			col_channel
	)

Get a 3D dataset from the defined ROI regions.

Returns a cell(s) imgOut 3D stacks of the shown ROIs

Parameters

type	type of the dataset to retrieve, image, model, mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
handles	handles of im_browser.m
roiNo	[optional] number of ROI to get, when omitted or NaN (default) take the currently selected ROIs. When 0 take all ROIs. Also it is possible to define ROI by its label as string of chars.
options	[optional], a structure with extra parameters .fillBg -> when NaN (default) -> crops the dataset as a rectangle; when a number fills the areas out of the ROI area with this intensity number .t -> current, time point to get a 3D dataset
col_channel	[optional], when type is image, col_channel is a vector with color numbers to take, , when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material will have index = 1.

Return values

imgOut

a cell array with 3D datasets from each selected ROI

Required fields of handles:

Required fields of options:

Examples:

imgOut = imageData.getRoiCrop('image', handles, 2);      // get the whole dataset under ROI 2 as rectangle image 

imgOut = imageData.getRoiCrop('image', handles, 2, options.fillBg=255);  // get the whole dataset under  ROI 2 as rectangle image with areas outside the roi filled with 255 intensity 

imgOut = getRoiCrop(obj, 'model', handles, 0);      // Call within the class; get all ROIs from the Model layer  

Attention

imgOut - is a cell object that can be accessed as

imgOut{index}(1:height,1:width,1:color,1:z) 

Implemented only for the XY plane

It is possible to use ib_getDataset.m wrapper function that takes into account shown ROIs

function imgOut = imageData.getRoiCropSlice	(		type,
			handles,
			roiNo,
			sliceNo,
			orient,
			options,
			col_channel
	)

Get a 2D slice of the ROI regions only.

Returns a cell(s) imgOut with 2D stacks of the shown ROIs.

Parameters

type	type of the dataset to retrieve, image, model, mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
handles	handles of im_browser.m
roiNo	[optional] number of ROI to get, when omitted or NaN (default) take the currently selected ROIs. When 0 take all ROIs. Also it is possible to define ROI by its label as string of chars.
sliceNo	[optional], number of the slice to get, when omitted or NaN returns the current slice
orient	[optional], get a slice in the desired orientation 1 - xz 2 - yz 4 - xy NaN - currently selected orientation
options	[optional], a structure with extra parameters .fillBg -> when NaN (default) -> crops the dataset as a rectangle; when a number fills the areas out of the ROI area with this intensity number.
col_channel	[optional], when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material will have index = 1.

Return values

imgOut

a cell array containing 3D images of ROIs. For the image type: [1:height, 1:width, 1:colors]; for all other types: [1:height, 1:width]

Required fields of handles:

Required fields of options:

Examples:

imgOut = handles.Img{handles.Id}.I.getRoiCropSlice('image', handles, 2);      // get ROI 2 as rectangle image, from the current slice.  

imgOut = handles.Img{handles.Id}.I.getRoiCropSlice('image', handles, 2, NaN, NaN, options.fillBg=255);  // get ROI 2 as rectangle image with areas outside the roi filled with 255 intensity, from the current slice. 

imgOut = obj.getRoiCropSlice('model', handles, 0);      // Call within the class; get all ROIs from the currently shown Model layer  

Attention

imgOut - is a cell object that can be accessed as

imgOut{index}(1:height,1:width,1:color)

It is possible to use ib_getSlice.m wrapper function that takes into account shown ROIs

function slice = imageData.getSlice	(		type,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

Get the 2D slice.

Parameters

type	type of the slice to retrieve, image, model,mask, selection, custom (custom indicates to use custom_img as the dataset), everything(model,mask and selection for imageData.model_type=='uint6' only)
slice_no	[optional], an index of the slice to show, when NaN will show the current slice
orient	[optional], can be NaN when 0 (default) returns the dataset transposed to the current orientation (obj.orientation) when 1 returns transposed dataset to the zx configuration: [y,x,c,z,t] -> [x,z,c,y,t] when 2 returns transposed dataset to the zy configuration: [y,x,c,z,t] -> [y,z,c,y,t] when 3 not used when 4 returns original dataset to the yx configuration: [y,x,c,z,t] when 5 not used
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.
custom_img	[optional], can be NaN; the function return a slice not from the imageData class but from this custom_img, requires to specify the custom type. custom_img should be a 3D dataset.
options	[optional], a structure with extra parameters .y -> [optional], [ymin, ymax] of the part of the slice to take .x -> [optional], [xmin, xmax] of the part of the slice to take .t -> [optional], [tmin, tmax] indicate the time point to take, when missing return the currently selected time point

Return values

slice

2D image. For the image type: [1:height, 1:width, 1:colors]; for all other types: [1:height, 1:width]

Examples:

slice = handles.Img{handles.Id}.I.getSlice('image', 5);      // get the 5-th slice of the current stack orientation  

slice = handles.Img{handles.Id}.I.getSlice('image', 5, 4, 2); // get the 5-th slice of the XY-orientation, color channel=2 

slice = handles.Img{handles.Id}.I.getSlice('custom', 5, 1, 2, custom_img); // get the 5-th slice of the YZ-orientation, color channel=2 from the custom_image 

slice = obj.getSlice(img, 'image', 5);      // Call within the class; get the 5-th slice of the current stack orientation  

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getSlice.m wrapper function, as

slice = ib_getSlice('image', handles) or imageData.getData2D 

function slice = imageData.getSliceToShow	(		type,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

Get a part of the 3D slice that fits into the viewing window of the handles.imageAxes, Note! the image will be cropped.

Parameters

type	type of the slice to retrieve, image, model,mask, selection, custom (custom indicates to use custom_img as the dataset), everything(model,mask and selection for imageData.model_type=='uint6' only)
slice_no	[optional], an index of the slice to show, when empty or NaN will show the current slice
orient	[optional], define orientation of the slice in the dataset when 1 - xz when 2 - yz when 4 - xy when NaN - current orientation
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.
custom_img	[optional], can be NaN; the function return a slice not from the imageData class but from this custom_img, requires to specify the custom type. custom_img should be a 3D dataset.
options	[optional], a structure with extra parameters .y -> [optional], [ymin, ymax] of the part of the slice to take .x -> [optional], [xmin, xmax] of the part of the slice to take .t -> [optional], [tmin, tmax] the time point of the dataset; default is the currently shown time point

Return values

slice

cropped 2D image. For the image type: [1:height, 1:width, 1:colors]; for all other types: [1:height, 1:width]

Required fields of options:

Examples:

slice = handles.Img{handles.Id}.I.getSliceToShow('image', 5);      // get the 5-th slice of the current stack orientation  

slice = handles.Img{handles.Id}.I.getSliceToShow('image', 5, 4, 2); // get the 5-th slice of the XY-orientation, color channel=2 

slice = handles.Img{handles.Id}.I.getSliceToShow('custom', 5, 1, 2, custom_img); // get the 5-th slice of the YZ-orientation, color channel=2 from the custom_image 

slice = getSliceToShow(obj, 'image', 5);      // Call within the class; get the 5-th slice of the current stack orientation  

Attention

not sensitive to the

obj. blockModeSwitch 

not sensitive to the shown ROI

References height, and width.

function imageData.insertEmptyColorChannel

(

channel1

)

Insert an empty color channel to the specified position.

Parameters

channel1

[optional] the index of color channel to insert.

Examples:

imageData.insertEmptyColorChannel(1);     // insert empty color channel to position 1 

insertEmptyColorChannel(obj, 1); // Call within the class; insert empty color channel to position 1 

References mib_inputdlg(), and updateImgInfo().

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function handles = imageData.insertSlice	(		img,
			handles,
			insertPosition,
			img_info
	)

Insert a slice or a dataset into the existing volume.

Parameters

img	new 2D-4D image stack to insert
handles	handles structure from im_browser
insertPosition	[optional] position where to insert the new slice/volume starting from 1. When omitted or NaN add img to the end of the dataset
img_info	[optional] containers Map with parameters of the dataset to insert

Return values

handles

handles structure from im_browser

Required fields of handles:

Examples:

handles = imageData.insertSlice(img, handles, 1);     // insert img to the beginning of the opened dataset 

handles = insertSlice(obj, img); // Call within the class; add img to the end of the opened dataset 

References img, img_info, mib_inputdlg(), and updateGuiWidgets().

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function imageData.invertColorChannel

(

channel1

)

Invert color channel of the dataset.

The specified channel1 will be inverted

Parameters

channel1

[optional] index of the color channel to invert

Examples:

handles = imageData.invertColorChannels(1);     // invert color channel 1 

handles = invertColorChannels(obj, 1); // Call within the class; invert color channel 1 

References mib_inputdlg(), and updateImgInfo().

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function imageData.mark2selection	(		layer_id,
			type,
			str_type,
			xy_vec
	)

Add a marker/pointer to the selection layer.

Parameters

layer_id	Index of the z-slice, for example (1)
type	a type of the marker: 'retract' - a minus sign, 'growth' - a plus sign 'sliding' - the x sign 'cross' - a cross sign 'large cross' - a larger cross sign
str_type	an additional identifier: 'tube' - draw a line on the left side of the marker 'sheet' - draw a line of the right side of the marker 'unknown' - keep the marker without line
xy_vec	- coordinates of the markers, [1:number of points, [x, y]]

Examples:

xy_vec(1, :) = [50 75];  

imageData.mark2selection(1, 'cross', '', xy_vec); // Draw a small cross at X=50 Y=75 

mark2selection(obj, 1, 'cross', '', xy_vec); // Call within the class 

Attention

Implemented only for the XY-orientation

function imageData.moveMaskToSelectionDataset	(		action_type,
			options
	)

Move the Mask layer to the Selection layer.

This is one of the specific functions to move datasets between the layers. Allows faster move of complete datasets between the layers than using of ib_getDataset.m / ib_setDataset.m functions.

Parameters

action_type	a type of the desired action 'add' - add mask to selection 'remove' - remove mask from selection 'replace' - replace selection with mask
options	a structure with additional paramters .contSelIndex - index of the Select from material .contAddIndex - index of the Add to material .selected_sw - [0 / 1] switch to limit actions to the selected Select from material only .maskedAreaSw - [0 / 1] switch to limit actions to the masked areas

Required fields of options:

Examples:

options.contSelIndex = get(handles.segmSelList,'Value')-2; // index of the selected material
options.contAddIndex = get(handles.segmAddList,'Value')-2; // index of the target material
options.selected_sw = get(handles.segmSelectedOnlyCheck,'value');   // when 1- limit selection to the selected material
options.maskedAreaSw = get(handles.maskedAreaCheck,'Value');

imageData.moveMaskToSelectionDataset('add', options);     // add mask to selection  

moveMaskToSelectionDataset(obj, 'add', options);     // call from the imageData class, add mask to selection  

Attention

NOT sensitive to the imageData.blockModeSwitch

NOT sensitive to the shown ROI

See Also

imageData.moveMaskToSelectionDataset imageData.moveModelToMaskDataset imageData.moveModelToSelectionDataset imageData.moveSelectionToMaskDataset imageData.moveSelectionToModelDataset

function imageData.moveModelToMaskDataset	(		action_type,
			options
	)

Move the selected Material to the Mask layer.

This is one of the specific functions to move datasets between the layers. Allows faster move of complete datasets between the layers than using of ib_getDataset.m / ib_setDataset.m functions.

Parameters

action_type	a type of the desired action 'add' - add the selected material (Select from) to mask 'remove' - remove the selected material (Select from) from mask 'replace' - replace mask with the selected (Select from) material
options	a structure with additional paramters .contSelIndex - index of the Select from material .contAddIndex - index of the Add to material .selected_sw - [0 / 1] switch to limit actions to the selected Select from material only .maskedAreaSw - [0 / 1] switch to limit actions to the masked areas

Required fields of options:

Examples:

options.contSelIndex = get(handles.segmSelList,'Value')-2; // index of the selected material
options.contAddIndex = get(handles.segmAddList,'Value')-2; // index of the target material
options.selected_sw = get(handles.segmSelectedOnlyCheck,'value');   // when 1- limit selection to the selected material
options.maskedAreaSw = get(handles.maskedAreaCheck,'Value');

imageData.moveModelToMaskDataset('add', options);     // add material to mask 

moveModelToMaskDataset(obj, 'add', options);     // call from the imageData class, add material to mask 

Attention

NOT sensitive to the imageData.blockModeSwitch

NOT sensitive to the shown ROI

See Also

imageData.moveMaskToSelectionDataset imageData.moveModelToMaskDataset imageData.moveModelToSelectionDataset imageData.moveSelectionToMaskDataset imageData.moveSelectionToModelDataset

function imageData.moveModelToSelectionDataset	(		action_type,
			options
	)

Move the selected Material to the Selection layer.

This is one of the specific functions to move datasets between the layers. Allows faster move of complete datasets between the layers than using of ib_getDataset.m / ib_setDataset.m functions.

Parameters

action_type	a type of the desired action 'add' - add the selected material (Select from) to selection 'remove' - remove the selected material (Select from) from selection 'replace' - replace selection with the selected (Select from) material
options	a structure with additional paramters .contSelIndex - index of the Select from material .contAddIndex - index of the Add to material .selected_sw - [0 / 1] switch to limit actions to the selected Select from material only .maskedAreaSw - [0 / 1] switch to limit actions to the masked areas

Required fields of options:

Examples:

options.contSelIndex = get(handles.segmSelList,'Value')-2; // index of the selected material
options.contAddIndex = get(handles.segmAddList,'Value')-2; // index of the target material
options.selected_sw = get(handles.segmSelectedOnlyCheck,'value');   // when 1- limit selection to the selected material
options.maskedAreaSw = get(handles.maskedAreaCheck,'Value');

imageData.moveModelToSelectionDataset('add', options);     // add material to selection 

moveModelToSelectionDataset(obj, 'add', options);     // call from the imageData class, add material to selection 

Attention

NOT sensitive to the imageData.blockModeSwitch

NOT sensitive to the shown ROI

See Also

imageData.moveMaskToSelectionDataset imageData.moveModelToMaskDataset imageData.moveModelToSelectionDataset imageData.moveSelectionToMaskDataset imageData.moveSelectionToModelDataset

function imageData.moveSelectionToMaskDataset	(		action_type,
			options
	)

Move the Selection layer to the Mask layer.

This is one of the specific function to move datasets between the layers. Allows faster move of complete datasets between the layers than using of ib_getDataset.m / ib_setDataset.m functions.

Parameters

action_type	a type of the desired action 'add' - add selection to mask 'remove' - remove selection from mask 'replace' - replace mask with selection
options	a structure with additional paramters .contSelIndex - index of the Select from material .contAddIndex - index of the Add to material .selected_sw - [0 / 1] switch to limit actions to the selected Select from material only .maskedAreaSw - [0 / 1] switch to limit actions to the masked areas

Required fields of options:

Examples:

options.contSelIndex = get(handles.segmSelList,'Value')-2; // index of the selected material
options.contAddIndex = get(handles.segmAddList,'Value')-2; // index of the target material
options.selected_sw = get(handles.segmSelectedOnlyCheck,'value');   // when 1- limit selection to the selected material
options.maskedAreaSw = get(handles.maskedAreaCheck,'Value');

imageData.moveSelectionToMaskDataset('add', options);     // add selection to mask  

moveSelectionToMaskDataset(obj, 'add', options);     // call from the imageData class, add selection to mask  

Attention

NOT sensitive to the imageData.blockModeSwitch

NOT sensitive to the shown ROI

See Also

imageData.moveMaskToSelectionDataset imageData.moveModelToMaskDataset imageData.moveModelToSelectionDataset imageData.moveSelectionToMaskDataset imageData.moveSelectionToModelDataset

function imageData.moveSelectionToModelDataset	(		action_type,
			options
	)

Move selection layer to the model layer.

This is one of the specific functions to move datasets between the layers. Allows faster move of complete datasets between the layers than using of ib_getDataset.m / ib_setDataset.m functions.

Parameters

action_type	a type of the desired action 'add' - add selection to the selected material (Add to) 'remove' - remove selection from the model 'replace' - replace the selected (Add to) material with selection
options	a structure with additional paramters .contSelIndex - index of the Select from material .contAddIndex - index of the Add to material .selected_sw - [0 / 1] switch to limit actions to the selected Select from material only .maskedAreaSw - [0 / 1] switch to limit actions to the masked areas

Required fields of options:

Examples:

options.contSelIndex = get(handles.segmSelList,'Value')-2; // index of the selected material
options.contAddIndex = get(handles.segmAddList,'Value')-2; // index of the target material
options.selected_sw = get(handles.segmSelectedOnlyCheck,'value');   // when 1- limit selection to the selected material
options.maskedAreaSw = get(handles.maskedAreaCheck,'Value');

imageData.moveSelectionToModelDataset('add', options);     // add selection to model  

moveSelectionToModelDataset(obj, 'add', options);     // call from the imageData class, add selection to model  

Attention

NOT sensitive to the imageData.blockModeSwitch

NOT sensitive to the shown ROI

See Also

imageData.moveMaskToSelectionDataset imageData.moveModelToMaskDataset imageData.moveModelToSelectionDataset imageData.moveSelectionToMaskDataset imageData.moveSelectionToModelDataset

function imageData.moveView	(		x,
			y,
			orient
	)

Center the image view at the provided coordinates: x, y.

Parameters

x	- X coordinate of the window center, or index of the point
y	- [optional] Y coordinate of the window center, can be NaN
orient	- [optional] define orientation of the point, default is the currently shown orientation when 0 (default) assumes that the points are taken at the current orientation (obj.orientation) when 1 assumes that the points are taken at the zx orientation when 2 assumes that the points are taken at the zy orientation when 3 not used when 4 assumes that the points are taken at the yx orientation when 5 not used

Examples:

imageData.moveView(50, 75);     // center the view at the pixel 50, 75 

moveView(obj, 75);// Call within the class; center the view at the pixel with index 75 

function handles = imageData.plotImage	(		axes,
			handles,
			resize,
			sImgIn
	)

Plot image to the axes. The main drawing function.

Parameters

axes	handle to axes, use handles.imageAxes
handles	handles structure from im_browser
resize	when 1 resize image to fit the screen when 0 keep the current vieweing settings
sImgIn	a custom 2D image to show in the axes that should be targeted to the axes. Use resize=0 to show sImgIn in the same scale/position as the currently shown dataset, or resize=1 to show sImgIn in full resolution

Return values

handles

- handles of im_browser.m

Required fields of handles:

Examples:

imageData.plotImage(handles.imageAxes, handles, 1);     // plot image in the handles.imageAxes axes and resize it 

handles = plotImage(obj, handles.imageAxes, handles, 1);// Call within the class; plot image in the handles.imageAxes axes and resize it 

References getRGBimage(), getRGBvolume(), and ib_updateCursor().

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function handles = imageData.replaceDataset	(		img,
			handles,
			img_info,
			modelImg,
			maskImg,
			selectionImg
	)

Replace existing dataset with a new one.

Parameters

img	a new 2D/3D image stack
handles	handles structure from im_browser
img_info	[optional] a containers.Map class with parameters of the dataset, can be NaN
modelImg	[optional] the Model layer, can be NaN
maskImg	[optional] the Mask layer, can be NaN
selectionImg	[optional] the Selection layer

Return values

handles

handles structure from im_browser

Required fields of handles:

Generated fields of handles:

Examples:

handles = imageData.replaceDataset(img, handles, img_info);     // replace the imageData.img with new stack from img  

handles = replaceDataset(obj, img, handles, img_info); // Call within the class; replace the imageData.img with new stack from img  

References ib_updatePixSizeAndResolution(), img, img_info, makeViewMatrix(), maskImg, updateAxesLimits(), and updateGuiWidgets().

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function handles = imageData.replaceImageColor	(		handles,
			type
	)

Replace image intensities in the Masked or Selected areas with new intensity value.

The function starts a dialog that asks for a new intensity values to replace either the Masked or Selected areas.

Parameters

handles	handles of im_browser.m
type	specifies which layer to use for color replacement: 'mask' or 'selection'

Return values

handles

handles of im_browser.m

Required fields of handles:

Examples:

handles = imageData.replaceImageColor(handles, 'mask');  // to replace the Masked areas with new color 

handles = replaceImageColor(obj, handles, 'selection');   // Call within the class; to replace the Selected areas with new color 

References ib_do_backup().

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function imageData.resizeImage	(		new_width,
			new_height,
			method
	)

Resize all layers using specified method.

Parameters

new_width	new width of the dataset
new_height	new height of the dataset
method	a method to use during resizing: 'nearest', 'bilinear', 'bicubic'

Note

The Model, Mask, Selection layers will be resized using the 'nearest' method.

Examples:

imageData.resizeImage(512, 1024);     // resize image to 512 width and 1024 height 

resizeImage(obj, 512, 1024);// Call within the class; resize image to 512 width and 1024 height 

function imageData.rotateColorChannel

(

channel1

)

Rotate color channel of the dataset.

The specified channel1 will be rotated

Parameters

channel1

[optional] index of the color channel to invert

Examples:

handles = imageData.rotateColorChannel(1);     // rotate color channel 1 

handles = handles.Img{handles.Id}.I.rotateColorChannel(1);     // rotate color channel 1 

handles.Img{handles.Id}.I.

handles = rotateColorChannel(obj, 1); // Call within the class; rotate color channel 1 

References mib_inputdlg().

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function imageData.setCurrentSlice	(		type,
			slice,
			color_id
	)

Update the currently shown slice of the dataset.

Parameters

type	type of the dataset to update, image, model, mask, selection, everything(model,mask and selection for imageData.model_type=='uint6' only)
slice	a new 2D slice, for the 'image' type [1:height,1:width, 1:color], for other latyers [1:height,1:width]
color_id	[optional], when type is image, color_id is a vector with color numbers to set, otherwise will update the colors selected in the imageData.slices{3} variable when type is model color_id may be 0 - to update all materials of the model or an integer to update specific material.

Examples:

imageData.setCurrentSlice('image', slice);      // update the currently shown image with data in slice 

imageData.setCurrentSlice('model', slice, 4); // replace material 4 with contents of slice 

slice = imageData.getCurrentSlice('model', 4); // get material 4 

imageData.setCurrentSlice('model', slice, 1); // set it as material 1 

setCurrentSlice(obj, 'model', slice, 1); // Call within the class; set it as material 1 

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

for normal calls it is recommended to use ib_setSlice.m wrapper function, as

ib_setSlice('image', slice, handles); 

References setSlice().

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function result = imageData.setData2D	(		type,
			slice,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

set the 3D slice: height:width:colors to the dataset

Parameters

type	type of the slice to set, image, model,mask, selection, custom (custom indicates to use custom_img as the dataset), everything(model,mask and selection for imageData.model_type=='uint6' only)
slice	3D image. For the image type: [1:height, 1:width, 1:colors]; for all other types: [1:height, 1:width]
slice_no	[optional], an index of the slice to update, when NaN updates the current slice
orient	[optional], can be NaN when 0 (default) updates the dataset transposed from the current orientation (obj.orientation) when 1 returns transposed dataset from the zx configuration: [x,z,c,y,t] -> [y,x,c,z,t] when 2 returns transposed dataset from the zy configuration: [y,z,c,y,t] -> [y,x,c,z,t] when 3 not used when 4 returns original dataset from the yx configuration: [y,x,c,z,t] when 5 not used
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.
custom_img	[optional], can be NaN; the function return a slice not from the imageData class but from this custom_img, requires to specify the custom type. custom_img should be a 3D dataset.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - update the full dataset, 1 - update only the shown part) .y -> [optional], [ymin, ymax] of the part of the slice to set .x -> [optional], [xmin, xmax] of the part of the slice to set .t -> [optional], [tmin, tmax] indicate the time point to set, when missing return the currently selected time point

Return values

slice

3D image. For the image type: [1:height, 1:width, 1:colors]; for all other types: [1:height, 1:width]

Required fields of options:

Examples:

slice = handles.Img{handles.Id}.I.setData2D('image', slice, 5);      // set the 5-th slice of the current stack orientation  

slice = handles.Img{handles.Id}.I.setData2D('image', slice, 5, 4, 2); // set the 5-th slice of the XY-orientation, color channel=2 

slice = handles.Img{handles.Id}.I.setData2D('custom', slice, 5, 1, 2, custom_img); // set the 5-th slice of the YZ-orientation, color channel=2 from the custom_image 

slice = obj.setData2D(img, 'image', slice, 5);      // Call within the class; set the 5-th slice of the current stack orientation  

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getSlice.m wrapper function, as

slice = ib_getSlice('image', handles); 

function result = imageData.setData3D	(		type,
			dataset,
			time,
			orient,
			col_channel,
			options,
			custom_img
	)

Set the 4D dataset (height:width:colors:depth) into the 5D dataset.

Parameters

type	type of the dataset to set, image, model,mask, selection, custom (custom indicates to use custom_img as the dataset), everything(model,mask and selection for imageData.model_type=='uint6' only)
dataset	3D or 4D stack. For the image type: [1:height, 1:width, 1:colors, 1:depth]; for all other types: [1:height, 1:width, 1:thickness]
time	[optional], an index of the time point to show, when NaN gets the dataset for the current time point
orient	[optional], can be NaN when 0 (default) updates the dataset transposed from the current orientation (obj.orientation) when 1 returns transposed dataset from the zx configuration: [x,z,c,y,t] -> [y,x,c,z,t] when 2 returns transposed dataset from the zy configuration: [y,z,c,y,t] -> [y,x,c,z,t] when 3 not used when 4 returns original dataset from the yx configuration: [y,x,c,z,t] when 5 not used
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material in slice will have index = 1.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - update the full dataset, 1 - update only the shown part) .y -> [optional], [ymin, ymax] of the part of the dataset to take .x -> [optional], [xmin, xmax] of the part of the dataset to take .z -> [optional], [zmin, zmax] of the part of the dataset to take
custom_img	[optional], can be NaN; the function return a slice not from the imageData class but from this custom_img, requires to specify the custom type. custom_img should be a 3D/4D dataset.

Return values

result

-> 1 - success, 0 - error

Examples:

dataset = handles.Img{handles.Id}.I.setData3D('image', dataset);      // set the 4D dataset for the current time point, in the shown orientation  

dataset = handles.Img{handles.Id}.I.setData3D('image', dataset, 5, 4); // set the 4D dataset for the 5-th time point in the XY orientation 

dataset = handles.Img{handles.Id}.I.setData3D('selection', dataset, 5, 1, 2); // set the 5-th timepoint in the the XZ-orientation, color channel=2 

dataset = obj.setData3D(img, 'image', dataset, [], 4);      // Call within the class; set the 4D dataset for the current time point in the XY orientation  

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

for normal calls it is recommended to use ib_setDataset.m wrapper function, as

dataset = ib_setDataset('image', handles); 

function result = imageData.setData4D	(		type,
			dataset,
			orient,
			col_channel,
			options
	)

result = setData4D(obj, type, dataset, orient, col_channel, options) Set complete 5D dataset

Parameters

type	type of the dataset to update, image, model,mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
dataset	4D or 5D stack. For the image type: [1:height, 1:width, 1:colors, 1:depth, 1:time]; for all other types: [1:height, 1:width, 1:thickness, 1:time]
orient	[optional], can be NaN when 0 (default) updates the dataset transposed from the current orientation (obj.orientation) when 1 returns transposed dataset from the zx configuration: [x,z,c,y,t] -> [y,x,c,z,t] when 2 returns transposed dataset from the zy configuration: [y,z,c,y,t] -> [y,x,c,z,t] when 3 not used when 4 returns original dataset from the yx configuration: [y,x,c,z,t] when 5 not used
col_channel	[optional], when type is image, col_channel is a vector with color numbers to take, when NaN [default] take the colors selected in the imageData.slices{3} variable, when 0 - take all colors of the dataset. when type is model col_channel may be NaN - to take all materials of the model or an integer to take specific material. In the later case the selected material will have index = 1.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - update the full dataset, 1 - update only the shown part) .y -> [optional], [ymin, ymax] coordinates of the dataset to take after transpose, height .x -> [optional], [xmin, xmax] coordinates of the dataset to take after transpose, width .z -> [optional], [zmin, zmax] coordinates of the dataset to take after transpose, depth .t -> [optional], [tmin, tmax] coordinates of the dataset to take after transpose, time

Return values

result

-> 1 - success, 0 - error

Required fields of options:

Examples:

handles.Img{handles.Id}.I.setData4D('image', dataset);      // update the complete dataset in the shown orientation 

handles.Img{handles.Id}.I.setData4D('image', dataset, NaN, NaN, options.blockModeSwitch=1); // update the croped to the viewing window dataset, with shown colors 

handles.Img{handles.Id}.I.setData4D('image', dataset, 4, 2); // update complete dataset in the XY orientation with only second color channel 

obj.setData4D('image', dataset);      // Call within the class, update the complete dataset  

Attention

sensitive to the imageData.blockModeSwitch

not sensitive to the shown ROI

for normal calls it is recommended to use ib_getDataset.m wrapper function, as

dataset = ib_getDataset('image', handles); 

function result = imageData.setDataset	(		type,
			dataset,
			orient,
			col_channel,
			options
	)

Update complete 4D dataset, LEGACY function, please use imageData.setData3D instead!

Parameters

type	type of the dataset to update, image, model, mask, selection, everything (model,mask and selection for imageData.model_type=='uint6' only)
dataset	a 4D stack with images
orient	[optional], can be NaN when 0 (default) returns the dataset transposed to the current orientation (obj.orientation) when 1 returns transposed dataset to the zx configuration: [y,x,c,z] -> [x,z,c,y] when 2 returns transposed dataset to the zy configuration: [y,x,c,z] -> [y,z,c,y] when 3 not used when 4 returns original dataset to the yx configuration: [y,x,c,z] when 5 not used
col_channel	[optional], can be NaN; when type is image, col_channel is a vector with color numbers to set, when NaN [default] update set the colors selected in the imageData.slices{3} variable; when 0 - update all colors of the dataset. when type is model col_channel may be NaN - to update all materials of the model or an integer to update specific material.
options	[optional], a structure with extra parameters .blockModeSwitch -> override the imageData.blockModeSwitch (0 - update full dataset, 1 - update only the shown area) .y -> [optional], [ymin, ymax] of the part of the dataset to set; .x -> [optional], [xmin, xmax] of the part of the dataset to set .z -> [optional], [zmin, zmax] of the part of the dataset to set

Return values

result

-> 1 - success, 0 - error

Examples:

result = handles.Img{handles.Id}.I.setDataset('image', dataset);      // set the 4D dataset into 5D at the current time point  

result = handles.Img{handles.Id}.I.setDataset('image', dataset, 0, NaN, options.blockModeSwitch=1); // set the croped to the viewing window part of the dataset, with shown colors 

result = handles.Img{handles.Id}.I.setDataset('image', dataset, 1, 2); // set complete transposed (XZ) dataset with only second color channel 

result = obj.setDataset('image', dataset);      // Call within the class; set the complete dataset  

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

for normal calls it is recommended to use ib_setDataset.m wrapper function, as

ib_setDataset('image', dataset, handles); 

References time.

function custom_img = imageData.setFullSlice	(		type,
			slice,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

Update the full 2D slice of the dataset.

Parameters

type	type of the image to update, image, model, mask, selection, custom, 'everything (get model, selection and mask, when imageData.model_type==uint6')
slice	2D image, for image type: [1:height, 1:width, 1:color], and [1:height, 1:width] for all other layers
slice_no	[optional], number of the slice to set, when empty or NaN update the current slice
orient	[optional], update the slice in the desired orientation 1 - xz 2 - yz 4 - xy NaN - the current orientation
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to set, when NaN [default] update set the colors selected in the imageData.slices{3} variable; when 0 - update all colors of the dataset. when type is model col_channel may be NaN - to update all materials of the model or an integer to update specific material.
custom_img	[optional], can be NaN; update a slice not from the imageData class but from this custom_img (3D dataset), requires the custom type
options	[optional], a structure with extra parameters .y -> [optional], [ymin, ymax] of the part of the slice to take .x -> [optional], [xmin, xmax] of the part of the slice to take .t -> [optional], [tmin, tmax] the time point of the dataset; default is the currently shown time point

Return values

custom_img

a modified 3D stack, for the 'custom' type, or 1 for success and 0 for an error of the function run

Required fields of options:

Examples:

imageData.setFullSlice('image', slice, 5);      // assign slice to the 5-th slice of the current stack orientation  

imageData.setFullSlice('image', slice, 5, 4, 2); // assign slice to the 5-th slice of the XY-orientation, color channel=2 

custom_img = imageData.setFullSlice('custom', slice, 5, 1, 2, custom_img); // assign slice to the 5-th slice of the YZ-orientation, color channel=2 to the custom_image 

setFullSlice(obj,'image', slice, NaN, NaN, 2); // Call within the class; assign slice to the current slice of the current orientation, color channel=2 

Attention

not sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

see also im_setSlice.m a wrapper function.

References height, and width.

Referenced by setSlice().

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function handles = imageData.setMaterialNames	(		modelMaterialNames,
			handles
	)

Set names for materials of the model.

Parameters

modelMaterialNames	a cell array with names for materials
handles	handles structure from im_browser

Return values

handles

handles structure from im_browser

Required fields of handles:

Example:

modelMaterialNames = {'Material 1','Material 2', 'Material 3'};   // define names for materials 

handles = imageData.setMaterialNames(modelMaterialNames);     // set material names  

handles = setMaterialNames(obj, modelMaterialNames); // Call within the class; set material names 

References model, modelMaterialNames, and updateSegmentationLists().

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function imageData.setRoiCrop	(		type,
			imgIn,
			handles,
			roiNo,
			options,
			col_channel
	)

Update a full 3D dataset from the defined ROI regions.

Note! Requires an array of cells as imgIn

Parameters

type	type of the image to update, image, model, mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
imgIn	a cell array with ROIs 3D volumes, imgIn{roiNo}(1:height,1:width,1:color,1:thickness)
handles	handles of im_browser.m
roiNo	[optional] number of ROI to update, when omitted or NaN take the currently selected. When 0 update all ROIs. Also it is possible to define ROI by its label as string of chars.
options	[optional], a structure with extra parameters .fillBg -> when 1 -> keep the background from imgIn; when NaN [default] -> crop imgIn with respect to the ROI shape .t -> current, time point to get a 3D dataset
col_channel	[optional], can be NaN; when type is image, col_channel is a vector with color numbers to update, when NaN [default] update set the colors selected in the imageData.slices{3} variable; when 0 - update all colors of the dataset. when type is model col_channel may be NaN - to update all materials of the model or an integer to update specific material.

Required fields of handles:

Required fields of options:

Examples:

imageData.setRoiCrop('image', imgIn, handles, 2);      // update whole dataset under ROI 2 as shaped ROI image.  

imageData.setRoiCrop('image', imgIn, handles, 2, NaN, NaN, options.fillBg=1);  // update whole dataset under ROI 2 as rectangle image with areas outside the roi filled with image intensity of imgIn. 

setRoiCrop(obj, 'model', imgIn, handles, 0);      // Call within the class; update whole Model dataset under all ROIs 

Attention

imgIn - is a cell object:

imgIn{index}(1:height,1:width,1:color,1:z) 

Implemented only for the XY plane

consider to use ib_setDataset.m wrapper function

function imageData.setRoiCropSlice	(		type,
			imgIn,
			handles,
			roiNo,
			sliceNo,
			orient,
			options,
			col_channel
	)

Update a 2D slice of the ROI regions of the dataset.

Note! Requires an array of cells as imgIn

Parameters

type	type of the image to update, image, model, mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
imgIn	a cell array with ROIs 2D slices, imgIn{roiNo}(1:height,1:width,1:color)
handles	handles of im_browser.m
roiNo	[optional] number of ROI to update, when omitted or NaN take the currently selected. When 0 take all ROIs. Also it is possible to define ROI by its label as string of chars.
sliceNo	[optional], a number of the slice to update, when omitted or NaN update the current slice
orient	[optional], update a slice in the desired orientation 1 - xz 2 - yz 4 - xy NaN - use the current orientation
options	[optional], a structure with extra parameters .fillBg -> when 1 -> keep the background from imgIn; when NaN [default] -> crop imgIn with respect to the ROI shape
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to update, when NaN [default] update set the colors selected in the imageData.slices{3} variable; when 0 - update all colors of the dataset. when type is model col_channel may be NaN - to update all materials of the model or an integer to update specific material.

Required fields of handles:

Required fields of options:

Examples:

handles.Img{handles.Id}.I.setRoiCropSlice('image', imgIn, handles, 2);      // update ROI 2 of the current slice as shaped ROI image.  

handles.Img{handles.Id}.I.setRoiCropSlice('image', imgIn, handles, 2, NaN, NaN, options.fillBg=1);  // update ROI 2 of the current slice as rectangle image with areas outside the roi filled with image intensity of imgIn. 

obj.setRoiCropSlice('model', imgIn, handles, 0);      // Call within the class; update all ROIs of the current Model layer  

Attention

imgIn - is a cell object: imgIn{index}(1:height,1:width,1:color)

consider to use ib_setSlice.m wrapper function

function custom_img = imageData.setSlice	(		type,
			slice,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

Update the 2D slice of the dataset.

Parameters

type	type of the image to update, image, model, mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
slice	2D image, for image as [1:height,1:width,1:color]; for other layers as [1:height,1:width]
slice_no	[optional] an index of the slice to update, when empty or NaN updates the current slice
orient	[optional] update a slice in the desired orientation 1 - xz 2 - yz 4 - xy NaN - use the current orientation
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to update, when NaN [default] update set the colors selected in the imageData.slices{3} variable; when 0 - update all colors of the dataset. when type is model col_channel may be NaN - to update all materials of the model or an integer to update specific material.
custom_img	[optional], can be NaN; update a slice not from the imageData class but from this custom_img (3D stack), requires the custom type
options	[optional], a structure with extra parameters .y -> [optional], [ymin, ymax] of the part of the slice to take .x -> [optional], [xmin, xmax] of the part of the slice to take .t -> [optional], [tmin, tmax] indicate the time point to take, when missing update the currently selected time point

Return values

custom_img

a modified 3D stack, for the custom type; or a status of the function run: - success, - fail.

Examples:

imageData.setSlice('image', slice, 5);      // set the 5-th slice of the current stack orientation  

imageData.setSlice('image', slice, 5, 4, 2); // set the 5-th slice of the XY-orientation, color channel=2 

custom_img = imageData.setSlice('custom', slice, 5, 1, 2, custom_img); // set the 5-th slice of the YZ-orientation, color channel=2 to the custom_image 

setSlice(obj, 'model', slice, 5, NaN, 2); // Call within the class; set the 5-th slice of the current orientation as the material 2 

Attention

sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

consider to use ib_setSlice.m wrapper function

References setFullSlice(), and setSliceToShow().

Referenced by setCurrentSlice().

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function custom_img = imageData.setSliceToShow	(		type,
			slice,
			slice_no,
			orient,
			col_channel,
			custom_img,
			options
	)

Update the croped to the viewing window 2D slice of the dataset.

Parameters

type	type of the image to update, image, model, mask, selection, or everything (model,mask and selection for imageData.model_type=='uint6' only)
slice	2D image, for image as [1:height,1:width,1:color]; for other layers as [1:height,1:width]
slice_no	[optional] an index of the slice to update, when empty or NaN updates the current slice
orient	[optional] update a slice in the desired orientation 1 - xz 2 - yz 4 - xy NaN - use the current orientation
col_channel	[optional], can be NaN when type is image, col_channel is a vector with color numbers to update, when NaN [default] update set the colors selected in the imageData.slices{3} variable; when 0 - update all colors of the dataset. when type is model col_channel may be NaN - to update all materials of the model or an integer to update specific material.
custom_img	[optional], can be NaN; update a slice not from the imageData class but from this custom_img (3D stack), requires the custom type
options	[optional], a structure with extra parameters .y -> [optional], [ymin, ymax] of the part of the slice to update .x -> [optional], [xmin, xmax] of the part of the slice to update .t -> [optional], [tmin, tmax] the time point of the dataset; default is the currently shown time point

Return values

custom_img

a modified 3D stack, for the custom type; or a status of the function run: - success, - fail.

Required fields of options:

Examples:

imageData.setSliceToShow('image', slice, 5);      // assign slice to the 5-th slice of the current stack orientation  

imageData.setSliceToShow('image', slice, 5, 4, 2); // assign slice to the 5-th slice of the XY-orientation, color channel=2 

custom_img = imageData.setSliceToShow('custom', slice, 5, 1, 2, custom_img); // assign slice to the 5-th slice of the YZ-orientation, color channel=2 to the custom_image 

setSliceToShow(obj, 'image', slice, NaN, NaN, 2); // Call within the class; assign slice to the current slice of the current orientation to color channel=2 

Attention

not sensitive to the

imageData.blockModeSwitch 

not sensitive to the shown ROI

consider to use ib_setSlice.m wrapper function

References height, and width.

Referenced by setSlice().

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function imageData.swapColorChannels	(		channel1,
			channel2
	)

Swap two color channels of the dataset.

The first color channel will be moved to the position of the second color channel, and the second color channel to the position of the first one

Parameters

channel1	[optional] index of the first color channel
channel2	[optional] index of the second color channel

Examples:

handles = imageData.swapColorChannels(1, 3);     // swap color channel 1 and 3 

handles = swapColorChannels(obj, 1, 3); // Call within the class; swap color channel 1 and 3 

References updateImgInfo().

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function imageData.transpose

(

new_orient

)

Change orientation of the image to the XY, XZ, or YZ plane.

Note

This function updates only the imageData.slices and imageData.orientation variables and do not rearrange the actual datasets.

Parameters

new_orient

a desired orientation: 1 -> XZ plane 2 -> YZ plane 3 -> YX plane

Examples:

imageData.transpose(1);      // transpose to the XZ plane  

transpose(obj, 1); // Call within the class; transpose to the XZ plane  

function handles = imageData.updateAxesLimits	(		handles,
			mode,
			newMagFactor
	)

Updates the imageData.axesX and imageData.axesY during fit screen, resize, or new dataset drawing.

Parameters

handles	handles structure from im_browser handles structure from im_browser
mode	update mode, resize -> scale to width/height zoom -> scale during the zoom
newMagFactor	a value of the new magnification factor, only for the zoom mode Return values:

Required fields of handles:

Examples:

handles = imageData.updateAxesLimits(handles, 'zoom', newMagFactor);     // update the axes using new magnification value 

handles = updateAxesLimits(obj, handles, 'resize'); // Call within the class; to fit the screen 

Referenced by replaceDataset().

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function imageData.updateBoundingBox	(		newBB,
			xyzShift,
			imgDims
	)

Update the bounding box info of the dataset.

The bounding box info is needed to properly put the dataset in the 3D space. It is encoded in the header of the Amira mesh file, or in the beginning of the ImageDescription field of the TIF file.

Parameters

newBB	- new Bounding Box parameters, Note! when NaN the dataset will be shifted with using xyzShift bb(1) = Xmin bb(2) = Width bb(3) = Ymin bb(4) = Height bb(5) = Zmin bb(6) = Thickness
xyzShift	[optional] a vector [height, width, z-stacks] with shifts of the bounding box; when omitted the function will use minimal parameters of the existing boinding box for the shitfs. Note! the units here are the image units: imageData.pixSize.units.
imgDims	[optional] a vector [height, width, z-stacks] with dimensions of the image; when omitted the function will use imageData.height, imageData.width and imageData.no_stacks variables. Note! the units here are the image units: imageData.pixSize.units.

Examples:

xyzShift = [10 5 0];  // shift the bounging box by 10 units in X, by 10 units in Y, and by 0 units in Z 

imageData.updateBoundingBox(NaN, xyzShift);  // get bounding box info 

updateBoundingBox(obj, NaN, xyzShift);   // Call within the class; get bounding box info 

newBB = [15 50 10 150 1 15];  // define new bounding box in imageData.pixSize.units 

imageData.updateBoundingBox(newBB);  // get bounding box info 

References no_stacks.

function imageData.updateDisplayParameters

(

)

Update display parameters for visualization.

The function updates imageData.viewPort structure. It is called from the imageAdjustment.m dialog.

Examples:

imageData.updateDisplayParameters();  // do update 

updateDisplayParameters(obj);   // Call within the class; do update 

function imageData.updateImgInfo	(		addText,
			action,
			entryIndex
	)

Update action log.

This function updates the image log with recent events done to the dataset; it updates the contents of imageData.img_info('ImageDescription') key.

Parameters

addText	a string that should be added to the log
action	[optional] - defines additional actions that may be performed with the log: 'delete' - delete entry defined with entryIndex 'insert' - insert new entry after the one defined with entryIndex 'modify' - modify entry with entryIndex
entryIndex	[optional] - index of the entry to delete, modify or insert

Examples:

slice = imageData.updateImgInfo('Image was filtered');      // Add 'Image was filtered' text into the imageData.img_info('ImageDescriotion')  

slice = imageData.updateImgInfo('','delete',4);      // Delete entry number 4 from the log  

slice = imageData.updateImgInfo('New entry inserted','insert',4);      // Insert new entry into the log at position 4 

slice = imageData.updateImgInfo('Updated text','modify',4);      // Modify text at position 4 

slice = updateImgInfo(obj, 'Image was filtered');      // Call within the class; Add 'Image was filtered' text into the imageData.img_info('ImageDescriotion')  

Referenced by copyColorChannel(), deleteColorChannel(), insertEmptyColorChannel(), invertColorChannel(), and swapColorChannels().

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function result = imageData.updateParameters

(

pixSize

)

Update imageData.pixelSize, imageData.img_info('XResolution') and imageData.img_info('XResolution')

The function starts a dialog to update voxel size and the units of the dataset. As result the voxel dimensions will be updated; in addition imageData.img_info('XResolution') and imageData.img_info('YResolution') keys will be recalculated.

Parameters

pixSize

- [optional], a structure with new parameters, may have the following fields .x - physical voxel size in X, a number .y - physical voxel size in Y, a number .z - physical voxel size in Z, a number .t - time difference between the frames, a number .units - physical units for voxels, (m, cm, mm, um, nm) .tunits - time unit

Required fields of pixSize:

Examples:

pixSize.x = 10;
pixSize.y = 10;
pixSize.z = 50;
pixSize.units = 'nm';
imageData.updateParameters(pixSize);  // update parameters using voxels: 10x10x50nm in size 

imageData.updateParameters();  // update parameters of the dataset 

updateParameters(obj);   // Call within the class; update parameters of the dataset 

References ib_calculateResolution(), and makeViewMatrix().

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Member Data Documentation

imageData.axesX

a vector [min, max] with minimal and maximal coordinates of the axes X of the imageAxes axes

imageData.axesY

a vector [min max] with minimal and maximal coordinates of the axes Y of the imageAxes axes

imageData.blockModeSwitch

defines whether to get the whole dataset or only the shown part of it, either 0 or 1

imageData.brush_prev_xy

coordinates of the previous pixel for the Brush tool,

Note

dimensions: [x, y] or NaN

imageData.brush_selection

selection layer during the brush tool movement,

{1:2}[1:height,1:width] or NaN 

brush_selection{1} - contains brush selection during drawing brush_selection{2} - contains labels of the supervoxels and some additional information .slic - a label image with superpixels .selectedSlic - a bitmap image of the selected with the Brush tool superpixels .selectedSlicIndices - indices of the selected Slic superpixels .selectedSlicIndicesNew - a list of freshly selected Slic indices when moving the brush, used for the undo with Ctrl+Z .CData - a copy of the shown in the imageAxes image, to be used for the undo brush_selection{3} - a structure that contains information for the adaptive mode: .meanVals - array of mean intensity values for each superpixels .mean - mean intensity value for the initial selection .std - standard deviation of intensities for the initial selection .factor - factor that defines variation of STD variation

Note

the brush_selection is modified with respect to

magFactor 

and crop of the image within the viewing window

imageData.colors

number of color channels

imageData.current_yxz

a vector to remember last selected slice number of each yx, zx, zy planes,

Note

dimensions:

[1 1 1] 

imageData.height

image height, px

Referenced by clearSelection(), getDatasetDimensions(), getFullSlice(), getSliceToShow(), setFullSlice(), and setSliceToShow().

imageData.hLabels

a handle to class to keep labels

imageData.hMeasure

a handle to class to keep measurements

imageData.hROI

handle to ROI class, roiImage

imageData.img

a property to keep the Image layer.

Note

The Image layer dimensions:

[1:height, 1:width, 1:colors 1:no_stacks] 

.

Referenced by addColorChannel(), clearContents(), clearSelection(), convertImage(), insertSlice(), and replaceDataset().

imageData.img_info

information about the dataset, an instance of the containers.Map class Default keys:

• ColorType - 'grayscale'
• ImageDescription - ''
• Height - 1
• Width - 1
• Stacks - 1
• XResolution - 1
• YResolution - 1
• ResolutionUnit - 'Inch'
• Filename - 'none.tif'
• SliceName - [optional] a cell array with names of the slices; for combined Z-stack, it is a name of the file that corresponds to the slice. Dimensions of the array should be equal to the obj.no_stacks

Referenced by insertSlice(), and replaceDataset().

imageData.imh

handle for the currently shown image

imageData.Ishown

a property to keep the currently displayed image in RGB format

Note

Ishown dimensions:

[1:height, 1:width, 1:colors] % 

imageData.lutColors

a matrix with LUT colors [1:colorChannel, R G B], (0-1)

Referenced by addColorChannel().

imageData.magFactor

magnification factor for the currently shown image, 1=100%, 1.5 = 150%

imageData.maskExist

a switch to indicate presense of the Mask layer. Can be 0 (no model) or 1 (model exist)

imageData.maskImg

a property to keep the Mask layer

Note

The Mask dimensions are:

[1:height, 1:width, 1:no_stacks] 

When the imageData.model_type == 'uint6', imageData.maskImg = NaN

Referenced by replaceDataset().

imageData.maskImgFilename

file name of the Mask layer image

imageData.maskStat

Statistics for the Mask layer with the PixelList info returned by regionprops Matlab function.

imageData.model

model is a property to keep the Model layer

Note

The model dimensions are

[1:height, 1:width, 1:no_stacks] 

Referenced by setMaterialNames().

imageData.model_diff_max

maximal absolute value in the image model of the diff_map type

imageData.model_fn

model_fn is a property to keep filename of the Model layer

imageData.model_type

The type of a model.

• uint6 - a segmentation model with upto 63 materials; the Model, Mask and Selection layers stored in the same matrix, to decrease memory consumption;

  Note

  • 10000000 - bit responsible for the Selection layer
  • 01000000 - bit responsible for the Mask layer
  • 00111111 - bits responsible for the Model layer, the maximal number of Materials in this type of model is 63.

• uint8 - a segmentation model with upto 255 materials; the Model, Mask and Selection layers stored in separate matrices;
• int8 - a model layer that has intensities from -128 to 128.
• segm - segmentation, uint8 class
• diffmap - difference maps, int8 class

Referenced by createModel(), and imageData().

imageData.model_var

model_var is a variable name in the mat-file to keep the Model layer

imageData.modelExist

a switch to indicate presense of the Model layer. Can be 0 (no model) or 1 (model exist)

imageData.modelMaterialColors

a matrix of colors [0-1] for materials of the Model, [materialIndex, R G B]

imageData.modelMaterialNames

an array of strings to define names of materials of the Model

Referenced by getMaterialNames(), and setMaterialNames().

imageData.no_stacks

number of stacks in the dataset

Referenced by updateBoundingBox().

imageData.none

Description of events

when selected two or more curves

Events:

none

imageData.orientation

Orientation of the currently shown dataset,.

• 4 = the yz plane, default
• 1 = the zx plane
• 2 = the zy plane

imageData.pixSize

a structure with diminsions of voxels,

.x .y .z .t .tunits .units 

the fields are

• .x - physical width of a pixel
• .y - physical height of a pixel
• .z - physical thickness of a pixel
• .t - time between the frames for 2D movies
• .tunits - time units
• .units - physical units for x, y, z. Possible values: [m, cm, mm, um, nm]

imageData.selection

a property to keep the Selection layer

Note

The selection dimensions:

[1:height, 1:width, 1:no_stacks] 

When the imageData.model_type == 'uint6', imageData.selection = NaN

imageData.slices

coordinates of the shown slice borders

Note

dimensions are

([height, width, color, z],[min max]) 

• (1,[min max]) - height
• (2,[min max]) - width
• (3,[min max]) - colors , array of color channels to show, for example [1, 3, 4]
• (4,[min max]) - z - value
• (5,[min max]) - t - time point

imageData.storedSelection

a buffer to store selection with press of Ctrl+C button, and restore with Ctrl+V

Note

dimensions are

[1:height, 1:width] or NaN 

imageData.time

number of time points in the dataset

Referenced by getDataset(), getDatasetDimensions(), and setDataset().

imageData.trackerYXZ

starting point for the Membrane Click-tracer tool

imageData.viewPort

a structure

.min .max .gamma 

for image adjustment the fields are

• .min - a vector with minimal intensities for contrast adjustment
• .max - a vector with maximal intensities for contrast adjustment
• .gamma - a vector with gamma factor for contrast adjustment

  Note

  Dimensions of each field is

  [1:colors] 

imageData.volren

a structure with parameters for the volume rendering the fields are

• .viewer_matrix - a viewer matrix generated from the Rotation, Translation and Scaling vectors using makeViewMatrix function
• .previewScale - scaledown factor for dataset preview during volren
• .previewIng - scaled down image
• .showFullRes - switch whether or not render image in full resolution or just preview

imageData.width

image width, px

Referenced by clearSelection(), getDatasetDimensions(), getFullSlice(), getSliceToShow(), setFullSlice(), and setSliceToShow().

---

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

• Classes/@imageData/imageData.m
• Classes/@imageData/addColorChannel.m
• Classes/@imageData/clearContents.m
• Classes/@imageData/clearMask.m
• Classes/@imageData/clearSelection.m
• Classes/@imageData/convertDataToMouseCoordinates.m
• Classes/@imageData/convertImage.m
• Classes/@imageData/convertModel.m
• Classes/@imageData/convertMouseToDataCoordinates.m
• Classes/@imageData/copyColorChannel.m
• Classes/@imageData/createModel.m
• Classes/@imageData/cropDataset.m
• Classes/@imageData/deleteColorChannel.m
• Classes/@imageData/deleteSlice.m
• Classes/@imageData/generateModelColors.m
• Classes/@imageData/getBoundingBox.m
• Classes/@imageData/getCoordinatesOfShownImage.m
• Classes/@imageData/getCurrentSlice.m
• Classes/@imageData/getCurrentSliceNumber.m
• Classes/@imageData/getCurrentTimePoint.m
• Classes/@imageData/getData2D.m
• Classes/@imageData/getData3D.m
• Classes/@imageData/getData4D.m
• Classes/@imageData/getDataset.m
• Classes/@imageData/getDatasetDimensions.m
• Classes/@imageData/getDatasetSizeInBytes.m
• Classes/@imageData/getFullSlice.m
• Classes/@imageData/getMaterialNames.m
• Classes/@imageData/getRGBimage.m
• Classes/@imageData/getRoiCrop.m
• Classes/@imageData/getRoiCropSlice.m
• Classes/@imageData/getSlice.m
• Classes/@imageData/getSliceToShow.m
• Classes/@imageData/insertEmptyColorChannel.m
• Classes/@imageData/insertSlice.m
• Classes/@imageData/invertColorChannel.m
• Classes/@imageData/mark2selection.m
• Classes/@imageData/moveMaskToSelectionDataset.m
• Classes/@imageData/moveModelToMaskDataset.m
• Classes/@imageData/moveModelToSelectionDataset.m
• Classes/@imageData/moveSelectionToMaskDataset.m
• Classes/@imageData/moveSelectionToModelDataset.m
• Classes/@imageData/moveView.m
• Classes/@imageData/plotImage.m
• Classes/@imageData/replaceDataset.m
• Classes/@imageData/replaceImageColor.m
• Classes/@imageData/resizeImage.m
• Classes/@imageData/rotateColorChannel.m
• Classes/@imageData/setCurrentSlice.m
• Classes/@imageData/setData2D.m
• Classes/@imageData/setData3D.m
• Classes/@imageData/setData4D.m
• Classes/@imageData/setDataset.m
• Classes/@imageData/setFullSlice.m
• Classes/@imageData/setMaterialNames.m
• Classes/@imageData/setRoiCrop.m
• Classes/@imageData/setRoiCropSlice.m
• Classes/@imageData/setSlice.m
• Classes/@imageData/setSliceToShow.m
• Classes/@imageData/swapColorChannels.m
• Classes/@imageData/transpose.m
• Classes/@imageData/updateAxesLimits.m
• Classes/@imageData/updateBoundingBox.m
• Classes/@imageData/updateDisplayParameters.m
• Classes/@imageData/updateImgInfo.m
• Classes/@imageData/updateParameters.m