# TIRL, the Tensor Image Registration Library (FMRIB/Oxford; Python + two Cython extensions). FMRIB's FSL installer ships it (conda package
# fsl-tirl 3.6.3); not in Fedora.
#
# VERSION CAVEAT: this is 3.6.2, the newest tag FMRIB publishes (git.fmrib.ox.ac.uk/fsl/tirl). The installer's 3.6.3 has no public source: the
# GitHub repo that FMRIB's page points to (tirlworks/tirl) is not reachable and there is no PyPI project. Morgan chose 3.6.2 (2026-10-09).
# 3.6.2 predates NumPy 2 and does not work on it; Patch0 ports it (see the changelog). Licence is Apache-2.0 (the LICENSE file in the source and in
# FMRIB's own install), though the conda metadata says "FSL"; the extensions link only LAPACK/BLAS, so this lives in the FREE project.

%global pypi_name tirl

%global tirl_requires python3-numpy python3-scipy python3-attrdict3 python3-dask python3-dill python3-imagecodecs python3-imageio python3-joblib python3-matplotlib python3-nibabel python3-nlopt python3-numba python3-opencv python3-openslide python3-pillow python3-psutil python3-pygments python3-dateutil python3-pyyaml python3-scikit-image python3-scikit-learn python3-simpleitk python3-threadpoolctl python3-tifffile

Name:           python-%{pypi_name}
Version:        3.6.2
Release:        1%{?dist}
Summary:        TIRL - Tensor Image Registration Library

License:        Apache-2.0
URL:            https://git.fmrib.ox.ac.uk/fsl/tirl
Source0:        https://git.fmrib.ox.ac.uk/fsl/tirl/-/archive/%{version}/tirl-%{version}.tar.gz
Patch0:         python-tirl-numpy2.patch

BuildRequires:  python3-devel
BuildRequires:  gcc
BuildRequires:  gcc-c++
BuildRequires:  gcc-gfortran
BuildRequires:  lapack-devel
BuildRequires:  blas-devel
BuildRequires:  python3-Cython
BuildRequires:  %{tirl_requires}

%global _description %{expand:
TIRL registers images in arbitrary dimensions with linear and nonlinear transformations (including displacement fields and their inversion),
tensor and scalar images, many cost functions and optimisers, with a TImage/TField data model. Includes FSLInterpolator, a Cython port of
FLIRT's trilinear interpolation, and a field-inversion extension.}

%description %_description

%package -n python3-%{pypi_name}
Summary:        %{summary}
Requires:       %{tirl_requires}

%description -n python3-%{pypi_name} %_description

%prep
%autosetup -p1 -n tirl-%{version}
head -1 tirl/tirl | grep -q '^#!'
%py3_shebang_fix tirl/tirl

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files tirl

%check
%pyproject_check_import
# upstream ships no tests. Known-answer checks of what the NumPy 2 port touches, against the installed tree.
export PYTHONPATH=%{buildroot}%{python3_sitearch}
%{python3} -sP - <<'PY'
import numpy as np, warnings, pkgutil, importlib
warnings.simplefilter("ignore")
import tirl
# 1. FSLInterpolator: trilinear interpolation of a linear function is exact in the interior (it returns 0 on the last voxel index, like FLIRT)
from tirl.cmodules.fslinterpolator import fslinterpolator
i, j, k = np.meshgrid(np.arange(4), np.arange(5), np.arange(6), indexing="ij"); d = (2*i + 3*j + 5*k + 1).astype(np.float32)
c = np.array([[1.5, 2.25, 3.75], [0, 0, 0], [2.9, 3.1, 4.2]], np.float32)
got = np.asarray(fslinterpolator(d, c)); want = 2*c[:, 0] + 3*c[:, 1] + 5*c[:, 2] + 1
assert np.allclose(got, want, atol=1e-3), (got, want)
# 2. field inversion: the inverse of a constant displacement (1, 0.5) is (-1, -0.5) (np.product in finv.pyx broke this on NumPy 2)
from tirl.cmodules.finv import invert
n = 8; g = np.stack(np.meshgrid(np.arange(n), np.arange(n), indexing="ij")).reshape(2, -1).T.astype(float)
field = np.zeros((2, n, n)); field[0] = 1.0; field[1] = 0.5
out = np.asarray(invert(np.array([[3.0, 3.0], [4.0, 2.0]]), field, g))
assert np.allclose(out, [[-1, -1], [-0.5, -0.5]], atol=1e-6), out
# 3. image construction and round trip (np.float_ default dtype and can_cast on a Python int broke this on NumPy 2)
from tirl.timage import TImage
a = np.arange(20, dtype=np.float32).reshape(4, 5); im = TImage(a)
assert np.array_equal(np.asarray(im.data), a) and tuple(im.vshape) == (4, 5)
# 4. every module imports
bad = []
for m in pkgutil.walk_packages(tirl.__path__, "tirl."):
    try: importlib.import_module(m.name)
    except BaseException as e: bad.append((m.name, repr(e)[:80]))
assert not bad, bad
print("tirl known-answer checks passed;", len(list(pkgutil.walk_packages(tirl.__path__, "tirl."))), "modules import")
PY

%files -n python3-%{pypi_name} -f %{pyproject_files}
%license LICENSE NOTICE
%doc README.md CHANGELOG.md
%{_bindir}/tirl

%changelog
* Fri Oct 09 2026 Morgan Hough <morgan.hough@gmail.com> - 3.6.2-1
- Initial package: TIRL 3.6.2 from FMRIB's GitLab, NOT the 3.6.3 that FMRIB's FSL installer ships (no public source for 3.6.3).
- Patch0 ports 3.6.2 to NumPy 2 (Fedora 44 has 2.4): np.product -> np.prod (10 sites incl. finv.pyx), np.float_ -> np.float64, np.complex -> complex,
  np.bool -> bool, np.in1d -> np.isin, and domain.py's can_cast(python int, dtype) -> an iinfo bound. Mechanical and behaviour-preserving, 9 files.
  Unpatched on NumPy 2.4.6 (scratch chroot): finv.invert raises AttributeError (np.product) and TImage(np.zeros((4,4))) raises TypeError (can_cast);
  patched: both work, field inversion returns the exact negative of a constant displacement, 85 of 85 modules import.
- No upstream tests; %%check carries known-answer checks (interpolation exact, field inversion, TImage round trip, all modules import). No registration
  has been run end to end, so the optimisers and cost functions beyond import are untested.