readBigDataViewerFormat.m File Reference

Read completely the BigDataViewer format of Fiji into Matlab. More...

Functions
function [ img_info , I ] =	readBigDataViewerFormat (filename, orient, options)
	Read completely the BigDataViewer format of Fiji into Matlab. More...

Detailed Description

Read completely the BigDataViewer format of Fiji into Matlab.

Function Documentation

function [ img_info , I ] = readBigDataViewerFormat	(		filename,
			orient,
			options
	)

Read completely the BigDataViewer format of Fiji into Matlab.

The format description: http://fiji.sc/BigDataViewer#About_the_BigDataViewer_data_format

Parameters

filename	name of the file: xml or h5
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
options	[optional], a structure with extra parameters .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 .c -> [optional], [indices] coordinates of the dataset to take after transpose, depth .t -> [optional], [tmin, tmax] coordinates of the dataset to take after transpose, time .level -> [optional], magnification level of the pyramid: 1-for unbinned

Return values

img_info	containers.Map with metadata
I	[optional], a dataset

Required fields of options:

Examples:

img_info = readBigDataViewerFormat('mydataset.xml');  // read only metadata 

img_info = readBigDataViewerFormat('mydataset.h5');  // read only metadata directly from hdf5 dataset 

[img_info, I] = readBigDataViewerFormat('mydataset.xml');   // read both metadata and dataset 

References xml2struct().

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