Skip to content

Add support for .nii.gz #217

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

Merged
william-silversmith merged 6 commits into from
Dec 3, 2025
Merged

Add support for .nii.gz #217

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
5c0468b
Add support for .nii.gz
chourroutm Dec 2, 2025
eb99cbe
Update igneous_cli/cli.py
chourroutm Dec 2, 2025
a13d1f5
Update igneous_cli/cli.py
chourroutm Dec 2, 2025
35df809
Update cli.py
chourroutm Dec 2, 2025
d761efc
Fix indentation for NII file extension check
chourroutm Dec 2, 2025
3838a83
Fix indentation issues in cli.py
chourroutm Dec 3, 2025
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
10 changes: 6 additions & 4 deletions igneous_cli/cli.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -278,7 +278,7 @@ def downsample(
"""
factor = (2,2,1)
if volumetric:
factor = (2,2,2)
factor = (2,2,2)

if compress and compress.lower() in ("none", "false"):
compress = False
Expand Down Expand Up @@ -379,7 +379,7 @@ def xfer(
"""
factor = (2,2,1)
if volumetric:
factor = (2,2,2)
factor = (2,2,2)

if compress and compress.lower() in ("none", "false"):
compress = False
Expand Down Expand Up @@ -1874,7 +1874,7 @@ def create(
):
"""Create a Precomputed volume from another data source.

Supports: .npy, .h5/.hdf5, .nii, .nrrd, and .ckl files
Supports: .npy, .h5/.hdf5, .nii/.nii.gz, .nrrd, and .ckl files

Hopefully will support others such as TIFF in the future.
"""
Expand Down Expand Up @@ -1934,6 +1934,8 @@ def normalize_file_ext(filename):
filename, ext2 = os.path.splitext(filename)
if ext2 in ('.ckl', '.cpso'):
return ext2
elif ext2 == '.nii':
return ext2
elif ext2 == '':
return ext
ext = ext2
Expand Down Expand Up @@ -2053,4 +2055,4 @@ def purge(queuepath):
"""Delete all queued messages and zero out queue statistics."""
queuepath = normalize_path(queuepath)
tq = TaskQueue(queuepath)
tq.purge()
tq.purge()