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@@ -3,8 +3,9 @@ uuid = "274281c4-ae57-11e9-2014-65d3d5d9358c" | |
| authors = ["[email protected] <[email protected]>"] | ||
| version = "0.1.0" | ||
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| [compat] | ||
| julia = "1.1" | ||
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| [deps] | ||
| HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" | ||
| Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" | ||
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| [compat] | ||
| julia = "1.1" | ||
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| @@ -0,0 +1,107 @@ | ||
| #= | ||
| hdf5utils.jl | ||
| Utilities for reading HDF5 data files for the 2019 fastMRI challenge. | ||
| Code by Steven Whitaker | ||
| Documentation by Jeff Fessler | ||
| =# | ||
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| export h5_get_keys, h5_get_attributes, h5_get_ismrmrd | ||
| export h5_get_ESC, h5_get_RSS, h5_get_kspace | ||
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| using HDF5 | ||
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| """ | ||
| `h5_getkeys(filename::String)` | ||
| Get `names` from file. Returns a `?` | ||
| """ | ||
| function h5_get_keys(filename::String) | ||
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| return h5open(filename, "r") do file | ||
| names(file) | ||
| end | ||
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| end | ||
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| """ | ||
| `h5_get_attributes(filename::String)` | ||
| Get `attrs` from file. Returns a `Dict` | ||
| """ | ||
| function h5_get_attributes(filename::String) | ||
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| return h5open(filename, "r") do file | ||
| a = attrs(file) | ||
| attr = Dict{String,Any}() | ||
| for s in names(a) | ||
| attr[s] = read(a[s]) | ||
| end | ||
| attr | ||
| end | ||
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| end | ||
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| """ | ||
| `h5_get_ismrmrd(filename::String)` | ||
| Get ISMRM header data from file. Returns a `?` | ||
| """ | ||
| function h5_get_ismrmrd(filename::String) | ||
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| return h5read(filename, "ismrmrd_header") | ||
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| end | ||
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| """ | ||
| `h5_get_ESC(filename::String; T::DataType = ComplexF32)` | ||
| Return `Array` of ESC (emulated single coil) data from file. | ||
| HDF5.jl reads the data differently than Python's h5py. | ||
| This is significant because the fastMRI paper | ||
| says that the datasets have certain dimensionality, | ||
| but the dimensions are permuted in Julia compared to Python, | ||
| hence the calls to `permutedims` in the following functions. | ||
| """ | ||
| function h5_get_ESC(filename::String; T::DataType = ComplexF32) | ||
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| data = T.(h5read(filename, "reconstruction_esc")) | ||
| return permutedims(data, ndims(data):-1:1) | ||
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| end | ||
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| """ | ||
| `h5_get_RSS(filename::String; T::DataType = ComplexF32)` | ||
| Return `Array` of RSS (root sum of squares) data from file. | ||
| """ | ||
| function h5_get_RSS(filename::String; T::DataType = ComplexF32) | ||
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| data = T.(h5read(filename, "reconstruction_rss")) | ||
| return permutedims(data, ndims(data):-1:1) | ||
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| end | ||
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| """ | ||
| `h5_get_kspace(filename::String; T::DataType = ComplexF32))` | ||
| Return `Array` of kspace data from file. | ||
| """ | ||
| function h5_get_kspace(filename::String; T::DataType = ComplexF32) | ||
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| data = h5open(filename, "r") do file | ||
| readmmap(file["kspace"], Array{getcomplextype(file["kspace"])}) | ||
| end | ||
| return permutedims(T.(data), ndims(data):-1:1) | ||
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| end | ||
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| #= | ||
| Copied (basically) from | ||
| https://github.com/MagneticParticleImaging/MPIFiles.jl/blob/79711bf7af389f9e2dd4b0370e64040e5da1e193/src/Utils.jl#L33 | ||
| =# | ||
| function getcomplextype(dataset) | ||
| T = HDF5.hdf5_to_julia_eltype( | ||
| HDF5Datatype(HDF5.h5t_get_member_type(datatype(dataset).id, 0))) | ||
| return Complex{T} | ||
| end |