mibGetImages.m File Reference

Generate image dataset from the files structure and the img_info containers.Map. More...

Functions
function [ img , img_info ] =	mibGetImages (files, img_info, options)
	Generate image dataset from the files structure and the img_info containers.Map.

Detailed Description

Generate image dataset from the files structure and the img_info containers.Map.

Function Documentation

mibGetImages()

function [ img , img_info ] = mibGetImages	(		files,
			img_info,
			options )

Generate image dataset from the files structure and the img_info containers.Map.

Parameters

files	- > structure from getImageMetadata.m .object_type -> type of the data, 'movie', 'hdf5_image', 'image' .filename - filenames .seriesName -> name of the series for HDF5/Bioformats .height -> image height .width -> image width .color -> number of color channels .noLayers -> number of image slices in the file .imgClass -> class of the image, 'uint8','uint16'... .dim_xyczt -> dimensions for hdf5_image and Bioformats, AmiraMesh (binned version) .depth_start - > [optional], for Amira Mesh only, to take only specified sections .depth_end - > [optional], for Amira Mesh only, to take only specified sections .depth_step -> [optional], for Amira Mesh only, Z-step to take not all sections .xy_step -> [optional], for Amira Mesh only, XY-step, i.e. binning factor .resizeMethod -> [optional], for Amira Mesh only, resize method for binning the XY-dimension, 'nearest', 'bilinear', 'bicubic' .backgroundColor -> [optional], to define a color when generating a stack from images of different XY dimensions. Only files(1).background is needed .level -> level of the image pyramid to load or an inden within TIF container .xMin -> optional for loading of a region within the image, min X coordinate of the region to load .xMax -> optional for loading of a region within the image, max X coordinate of the region to load% .yMin -> optional for loading of a region within the image, min Y coordinate of the region to load .yMax -> optional for loading of a region within the image, max Y coordinate of the region to load .zMin -> optional for loading of a region within the image, min Z coordinate of the region to load .zMax -> optional for loading of a region within the image, max Z coordinate of the region to load .xyStep -> optional for loading of a region within the image, XY step, pixels between are skipped
img_info	-> containers.Map with details of the dataset from getImageMetadata()
options	-> structure with options .waitbar -> 0 - no waitbar, 1 - show waitbar .imgStretch [optional] -> stretch or not the image if it is uint32 class .silentMode [optional] -> when true - do not ask questions

Return values

img	-> image dataset [1:height, 1:width, 1:color, 1:z]
img_info	-> modified containers.Map with details of the dataset

Required fields of options:

References amiraMesh2bitmap(), loadBigDataViewerFormat(), max, mibInputMultiDlg(), min, nrrdLoadWithMetadata(), and uint32.

Referenced by mibRechopDatasetController.combineBtn_Callback(), mibAlignmentController.continueBtn_Callback(), mibLoadImages(), and mibWoundHealingAssayController.Stitch().

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