Get the 2D slice from the dataset, the wrapper function. More...

Functions
function slice =	ib_getSlice (type, handles, slice_no, orient, col_channel, options)
	Get the 2D slice from the dataset, the wrapper function. More...

Detailed Description

Get the 2D slice from the dataset, the wrapper function.

Function Documentation

function slice = ib_getSlice	(	type,
		handles,
		slice_no,
		orient,
		col_channel,
		options
	)

Get the 2D slice from the dataset, the wrapper function.

This is a wrapper function, it uses the functions of the imageData class to get a slice from the dataset. When ROIs regions are shown in the axes (handles.roiShowCheck checkbox) the function returns array of cells of only those ROI areas.

Attention: The return value is an array of cells!

Parameters

type	a type of the image to update, 'image', 'model', 'selection', 'mask', 'everything' (for imageData.model_type=='uint6' only)
handles	handles structure of im_browser.m
slice_no	[optional], a number of the slice to get, when empty or NaN get the currently shown slice
orient	[optional], get a slice in the desired orientation 0 (default) gets the slice transposed to the current orientation (obj.orientation) 1 - xz 2 - yz 4 - xy NaN - the current orientation
col_channel	[optional], when type is 'image', col_channel is a vector with color numbers to obtain, 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 object will have index = 1.
options	a structure with extra parameters .blockModeSwitch -> override the block mode switch imageData.blockModeSwitch - 0 get full dataset / 1 - get dataset crop .fillBg -> NaN->get ROI as a square; when .fillBg is an integer number, the script use this number to fill areas outside the ROI shape .roiId -> an index of ROI to use, when 0 - get all shown ROIs. Also it is possible to define ROI by its label as string .t -> [optional], [tmin, tmax] the time point of the dataset; default is the currently shown time point

Return values

slice an array of cells with 2D slices, format - slice{roiId}(1:height, 1:width, 1:color); roiId=1 when one or no ROI

Required fields of handles:

Required fields of options:

Referenced by ib_anisotropicDiffusion(), ib_contrastCLAHE(), ib_invertImage(), ib_linearContrast(), ib_maskGenerator(), ib_moveLayers(), ib_removeBackground(), ib_segmentation_SmartWatershed(), ib_sizeExclusionFilter(), imageFilterDoitBtn_Callback(), ibimageMorphOpsGui>continueBtn_Callback(), ibMorphOpsGui>continueBtn_Callback(), ManGridBW>ManGridBW_OpeningFcn(), ManGridBW>startBtn_Callback(), and ManGridBW>thresholdsTable_CellEditCallback().

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Functions

Detailed Description

Function Documentation