ENH: Update NrrdIO upstream with recent teem updates

[hjmjohnson]

Update for synchronizing with the upstream teem project

git clone https://git.code.sf.net/p/teem/nrrdio/nrrdio.git NrrdIO

This commit updates the ThirdParty NrrdIO library to the latest version
from the upstream Teem project. This update includes several
modernization efforts, bug fixes, and new features.

Major changes include:

1. A decade of NrrdIO updates.
2. Improved const-correctness
3. Replace unsafe funcitons (i.e. sprintf -> snprintf and similar)
4. Zero Run Length (ZRL) Encoding Support: Added a new encoding
   (encodingZRL.c) that supports reading ZRL-compressed NRRD files.
5. Script Modernization:
   • Replaced legacy Perl scripts (mangle.pl, tail.pl, unteem.pl)
     with Python equivalents (mangle.py, tail.py, unteem.py).
   • Added 0-gen.sh to provide a reliable, documented way to
     regenerate NrrdIO from Teem sources.
6. Code Style and Formatting:
   • Applied project-wide clang-format to improve consistency.
   • Added .clang-format configuration file to the source directory.
7. Refactoring and Cleanup:
   • Refactored NrrdIO.h and NrrdIO.h.in for better maintainability.
   • Removed obsolete files including dio.c, qnanhibit.c, and
     associated CMake tests.
   • Renamed 000-README.txt to 0-README.txt.
8. Build System Improvements:
   • Updated CMakeLists.txt to use modern CMake patterns.
   • Added ITK-specific library build requirements and installation
     rules for mangled headers.
9. Legal and Documentation:
   • Updated copyright notices to include 2026.
   • Clarified licensing in 0-README.txt and LICENSE.

These changes ensure that ITK's NRRD support remains compatible with
the latest upstream developments while improving the developer
experience for maintaining the third-party module.

PR Checklist

• No API changes were made (or the changes have been approved)
• No major design changes were made (or the changes have been approved)

[dzenanz]

This seems to work?

[hjmjohnson]

This seems to work?

Yes. I'm working with @kindlmann to move Teem and NrrdIO from SVN to git on SourceForge. What is included in this patch set is proposed testing for patch sets that are not yet included upstream in NrrdIO or Teem.

I was just waiting for the dust to settle in the upstream changes before finalizing this and linking it to the stable git hashes upstream.

[blowekamp]

Thank you for working on this.

When a new UpdateFromUpstream.sh process is added, as I recall the old code is usually deleted from the repo, then the directory is re-estabished with a sub-tree merge. So once the upstream work is completed, it does not need to be updated here before the new process is established.

[hjmjohnson]

Thank you for working on this.

When a new UpdateFromUpstream.sh process is added, as I recall the old code is usually deleted from the repo, then the directory is re-estabished with a sub-tree merge. So once the upstream work is completed, it does not need to be updated here before the new process is established.

@blowekamp This may not work for NrrdIO. The central part of the NrrdIO git repo is a set of scripts that extract code from the teem source code base and replace the LGPL license with a BSD license, drop chunks of code that exist in teem, but are not needed for NrrdIO, and create the mangling headers. It is starter code for other projects to adapt from, but not necessarily useful on its own.

The set of scripts that extract data from teem does different things when the "itk" flag is passed in, and the "itk" variant of the extracted code has specializations for ITK that are not part of the central git repository. I'm working with Gordon to create a single codebase that is easier to maintain, but I'm not sure we will get there.

[blowekamp]

I didn't see what occurs with running scripts with the itk variant in the repo:
https://sourceforge.net/p/teem/nrrdio/nrrdio.git/ci/main/tree/

But keep in mind the standard update script unarchived the git repo, and runs some scripts and command to clean up the code for the sub-tree commit. It sounds like the approach taken may still fit into the existing update framework. Here is an example of what happens for HDF5:

ITK/Modules/ThirdParty/HDF5/UpdateFromUpstream.sh

Line 38 in b182514

extract_source () {

[kindlmann]

I'm grateful for the continued work of @hjmjohnson on this, and I do believe "we will get there" as long as we keep communicating.

The new 0-gen.sh script in NrrdIO is a work-in-progress, but it's main goal is to (like Hans mentioned) do the necessary transformations of Teem source into a minimal set of NrrdIO sources. How much work it should do to anticipate ITK's subsequent use specifically, versus be configurable for any other application, is something I think we're still trying to determine. Anyone else interested is welcome to join the discussion at https://discord.gg/xBBqZGXkF7

[hjmjohnson]

FYI: This is still being pursued. Upstream teem modifications are ongoing, and more extensive than originally thought. This is all good, but is taking a bit longer than anticipated.