H5SectionsArrays.jl

cutout arbitrary chunks from a serials of 2D image sections in hdf5 format

• only support cutout, no writting
• used as normal Julia array
• support negative coordinate

Note that we only support UInt8 data type for now, should be easy to extend if neccesary.

Installation

Pkg.add("H5SectionsArrays")

Usage

using H5SectionsArrays
ba = H5SectionsArray("path/of/dataset/")
a = ba[101:300, -99:100, 1:3]

File format

The section format follows the convention of ImageRegistration.jl

a registry file

this file, called registry.txt should contain a few columns: filename 0 offset-x offset-y size-x size-y true.

here is an example:

2,33_aligned    0   -293    -344    56834   25126   true
2,34_aligned    0   -1352   -1761   59385   28240   true
2,35_aligned    0   -1291   -1438   58320   27505   true
2,36_aligned    0   -1907   -1471   59306   27474   true
2,37_aligned    0   -1912   -2105   59320   28603   true

a image section in hdf5 format

the hdf5 file should contain several datasets:

• img: the image array
• offset: a vector containing x,y offsets
• size: the size of the img dataset

For details please take a look of the test script runtests.jl, which construct a fake dataset.