Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add new_vol_like convenience function #60

Open
wants to merge 8 commits into
base: master
Choose a base branch
from
Open

Add new_vol_like convenience function #60

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
b2d29a2
Add new_vol_like
Jan 17, 2022
cdda2d5
fix merge conflicts
Mar 24, 2022
db663c5
Revert "fix merge conflicts"
Mar 24, 2022
22e25ad
further fixing
Jan 17, 2022
d79477f
Merge master changes
Jan 17, 2022
f0238a4
Merge branch 'new_vol_like' of github.com:clin045/NIfTI.jl into new_v…
Mar 24, 2022
4fda850
add test for new_vol_like
Mar 24, 2022
3a58f45
add test for extensions
Mar 24, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 10 additions & 1 deletion src/NIfTI.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ module NIfTI
using CodecZlib, Mmap, MappedArrays, TranscodingStreams

import Base.getindex, Base.size, Base.ndims, Base.length, Base.write, Base64
export NIVolume, niread, niwrite, voxel_size, time_step, vox, getaffine, setaffine
export NIVolume, niread, niwrite, voxel_size, time_step, vox, getaffine, setaffine, new_vol_like

include("parsers.jl")
include("extensions.jl")
Expand Down Expand Up @@ -176,6 +176,15 @@ function NIVolume(
(orientation[2, :]...,), (orientation[3, :]...,), string_tuple(intent_name, 16), NP1_MAGIC), extensions, raw)
end

"""
new_vol_like(vol::NIVolume{T}, raw::R) where {R,T}

Convenience function to create a new NIfTI volume with data `raw`, using
the header and extensions of `vol`.
"""
new_vol_like(vol::NIVolume{T}, raw::R) where {R,T} = NIVolume(vol.header,vol.extensions,raw)


# Validates the header of a volume and updates it to match the volume's contents
function niupdate(vol::NIVolume{T}) where {T}
vol.header.sizeof_hdr = SIZEOF_HDR1
Expand Down
8 changes: 8 additions & 0 deletions test/runtests.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,14 @@ const TEMP_GZIPPED_FILE = joinpath(TEMP_DIR_NAME, "$(tempname()).nii.gz")
niwrite(TEMP_GZIPPED_FILE, vol)
niread(TEMP_GZIPPED_FILE)

# Test new_img_like
img = niread(GZIPPED_NII)
test_raw = ones(size(img))
new_img = new_vol_like(img, test_raw)
@test new_img.header == img.header
@test new_img.raw == test_raw
@test new_img.extensions == img.extensions

# Write and read DT_BINARY
const BOOL_WRITE = joinpath(TEMP_DIR_NAME, "$(tempname()).nii")
const BIT_WRITE = joinpath(TEMP_DIR_NAME, "$(tempname()).nii")
Expand Down