# TIRL, the Tensor Image Registration Library (FMRIB/Oxford, by Istvan Huszar; Python plus two Cython extensions; histology-to-MRI and general
# image registration). FMRIB's FSL installer ships it as conda package fsl-tirl 3.6.3; not in Fedora.
#
# SOURCE: FMRIB publishes no 3.6.3 tag. Its project page (git.fmrib.ox.ac.uk/fsl/tirl) says development moved to GitHub (tirlworks/tirl, not
# reachable), and its tags stop at 3.6.2; but the author's own repository, git.fmrib.ox.ac.uk/ihuszar/tirl (public, branch master), is three commits
# past 3.6.2 and its master (commit 9b57d75, 2024-05-03) is what FSL ships: diffing FMRIB's installed 3.6.3 against that commit shows 82 files
# differing ONLY in the licence-header substitution plus __version__ "3.6.2" -> "3.6.3" and __license__ "FSL" -> "ApacheV2". %prep applies those
# two label changes. Licence is Apache-2.0 (LICENSE in the source and in FMRIB's install; conda metadata says "FSL"). The extensions link only
# LAPACK/BLAS, so this lives in the FREE project.
#
# Patch0 ports it to NumPy 2: FMRIB's own shipped 3.6.3 fails on their bundled NumPy 2.4.6 (TImage creation, finv.invert). Patch1 drops setup.py's
# install-time write into the installing user's ~/.config and its build-time import of tirl.

%global commit  9b57d75ad23588936abaee8184b4528ad4e272cb

%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:        3.6.3
Release:        1%{?dist}
Summary:        TIRL - Tensor Image Registration Library

License:        Apache-2.0
URL:            https://git.fmrib.ox.ac.uk/ihuszar/tirl
Source0:        https://git.fmrib.ox.ac.uk/ihuszar/tirl/-/archive/%{commit}/tirl-%{commit}.tar.gz
Patch0:         python-tirl-numpy2.patch
Patch1:         python-tirl-setup.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-%{commit}
# the release labelling FMRIB's FSL build applies to this commit (see the header): version and licence string only
grep -q '^__version__ = "3.6.2"' tirl/__init__.py
sed -i 's/^__version__ = "3.6.2"/__version__ = "%{version}"/' tirl/__init__.py
grep -q '^__license__ = "FSL"' tirl/__init__.py
sed -i 's/^__license__ = "FSL"/__license__ = "ApacheV2"/' tirl/__init__.py
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
assert tirl.__version__ == "%{version}", tirl.__version__
print("tirl known-answer checks passed;", len(list(pkgutil.walk_packages(tirl.__path__, "tirl."))), "modules import")
PY

# a build must not write into the builder's home (upstream's setup.py used to copy tirl.yml there)
test ! -e "$HOME/.config/tirl.yml"

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

%changelog
* Fri Oct 09 2026 Morgan Hough <morgan.hough@gmail.com> - 3.6.3-1
- Rebase on the source FSL actually ships: the author's repository git.fmrib.ox.ac.uk/ihuszar/tirl at commit 9b57d75 (2024-05-03), whose files differ
  from FMRIB's installed tirl 3.6.3 only in the licence-header substitution (82 files) and __version__/__license__. This supersedes 3.6.2-1, which was
  built from the fsl/tirl mirror because no 3.6.3 source had been found; the earlier note that 3.6.3 had no public source was wrong about where to look.
- Patch1 (setup.py): do not import tirl at build time and do not copy tirl.yml/tirlscripts.yml into the builder's ~/.config; both ship as %%doc.
- %%check also asserts the version and that the build wrote nothing under $HOME/.config.

* Fri Oct 09 2026 Morgan Hough <morgan.hough@gmail.com> - 3.6.2-1
- Initial package: TIRL 3.6.2 from FMRIB's GitLab mirror (the newest tag it publishes), with Patch0 porting it to NumPy 2 (np.product -> np.prod, 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; 9 files). Unpatched on
  NumPy 2.4.6: finv.invert raises AttributeError (np.product), 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.