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ImagineFormat

Read .imagine files in Julia

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ImagineFormat

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Imagine is an acquisition program for light sheet microscopy written by Zhongsheng Guo in Tim Holy's lab. This package implements a loader for the file format for the Julia programming language. Each Imagine "file" consists of two parts (as two separate files): a *.imagine file which contains the (ASCII) header, and a *.cam file which contains the camera data. The *.cam file is a raw byte dump, and is compatible with the NRRD "raw" file.

Usage

Read Imagine files like this:

using Images
img = load("filename")

Converting to NRRD

You can write an NRRD header (*.nhdr) from an Imagine header as follows:

h = ImagineFormat.parse_header(filename)  # the .imagine file name
imagine2nrrd(nrrdname, h, datafilename)

where datafilename is the name of the *.cam file. It is required by the *.nhdr file to point to the actual data.

Writing Imagine headers

You can use the non-exported function ImagineFormat.save_header:

save_header(destname, srcname, img, [T])

destname is the output *.imagine file; srcname is the name of the "template" file. Certain header values (e.g., size information) are updated by reference to img. The optional argument T allows you to specify a different element type than possessed by img.

First Commit

09/27/2015

Last Touched

2 months ago

Commits

62 commits

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