# scikit-build-core builds the extension through CMake and its debug sources
# are not tracked into debugsourcefiles.list (empty -> FTBFS), as with
# python-pymeshfix; disable the debug package.
%global debug_package %{nil}

%global pypi_name antspyx
# ANTsRCore commit holding the r64/r85 test slices ANTsPy downloads from figshare
# (byte-identical to the figshare copies; ANTsRCore is Apache-2.0 like ANTsPy).
%global antsrcore_commit 9a875df253d48e700d0cdf6be14bd60eba62fb6f

Name:           python-%{pypi_name}
Version:        0.6.3
Release:        2%{?dist}
Summary:        ANTsPy: Advanced Normalization Tools in Python

License:        Apache-2.0
URL:            https://github.com/ANTsX/ANTsPy
Source0:        %{url}/archive/v%{version}/ANTsPy-%{version}.tar.gz
Source1:        https://raw.githubusercontent.com/ANTsX/ANTsRCore/%{antsrcore_commit}/inst/extdata/r64slice.jpg
Source2:        https://raw.githubusercontent.com/ANTsX/ANTsRCore/%{antsrcore_commit}/inst/extdata/r85slice.jpg
# Build against system ITK and ANTs. Upstream's CMakeLists runs
# scripts/configure_ITK.sh and configure_ANTs.sh, which git-clone ITK 5.4.5 and
# ANTs b53aad3, build ITK statically and compile a private copy of 19 ANTs
# programs into the module. We link the same programs from ANTs' libl_*
# libraries instead (ANTs-devel >= 2.6.5-20 carries the b53aad3 backport).
Patch0:         python-antspyx-system-itk-ants.patch
# ants.get_data(): use the slices shipped in %%{_datadir}/antspyx before
# downloading them to ~/.antspy.
Patch1:         python-antspyx-system-data.patch

BuildRequires:  python3-devel
BuildRequires:  gcc-c++
BuildRequires:  cmake
BuildRequires:  ninja-build
BuildRequires:  ANTs-devel >= 2.6.5-20
BuildRequires:  InsightToolkit5-devel >= 5.4.7-24
# Re-found by ITK's module cmake files through ITK_USE_FILE (as in ANTs.spec).
BuildRequires:  hdf5-devel
BuildRequires:  libminc-devel
BuildRequires:  python3-pytest

%global _description %{expand:
ANTsPy is the Python interface to Advanced Normalization Tools (ANTs):
image registration (rigid, affine, SyN and the antsRegistrationSyN presets),
N3/N4 bias field correction, Atropos segmentation, cortical thickness
(KellyKapowski), joint label fusion, denoising and resampling, with images
held as NumPy-interoperable ANTsImage objects.

This build links the system ANTs and ITK libraries instead of the private
copies upstream's wheels compile in.}

%description %_description

%package -n python3-%{pypi_name}
Summary:        %{summary}
# The module shares ITK objects (images, transforms) with libITK* and libl_*:
# pin the ITK layout state, as ANTs does (see InsightToolkit5.spec).
Requires:       itk(abi) = %{?itk_abi}%{!?itk_abi:UNSET}

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

%prep
%autosetup -n ANTsPy-%{version} -p1
# Upstream caps numpy <2.4 and scipy <1.16 for its wheel matrix; Fedora ships
# numpy 2.4 and scipy 1.16, and the test suite below runs against them.
sed -i -e 's/"numpy<2.4.0"/"numpy"/' -e 's/"scipy<1.16"/"scipy"/' pyproject.toml
grep -q '^    "numpy",$' pyproject.toml
grep -q '^    "scipy"$' pyproject.toml
# The configure scripts must not run (they download); Patch0 removed the calls.
! grep -q configure_ CMakeLists.txt
# nanobind: upstream pins <2.6; the module builds with Fedora's 2.11.
sed -i 's/"nanobind >=1.3.2,<2.6"/"nanobind >=1.3.2"/' pyproject.toml

%generate_buildrequires
%pyproject_buildrequires

%build
test -n "%{?itk_abi}" || { echo "ERROR: itk_abi undefined - needs InsightToolkit5-devel >= 5.4.7-24 (macros.itk)" >&2; exit 1; }
export CMAKE_ARGS="-DITK_DIR:PATH=%{_prefix}/lib/cmake/ITK-5.4 -DCMAKE_BUILD_TYPE=RelWithDebInfo"
export CMAKE_BUILD_PARALLEL_LEVEL=%{_smp_build_ncpus}
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files -L ants
install -d %{buildroot}%{_datadir}/antspyx
install -p -m 0644 data/r16slice.jpg data/r27slice.jpg data/r30slice.jpg data/r62slice.jpg \
    %{SOURCE1} %{SOURCE2} %{buildroot}%{_datadir}/antspyx/

%check
%pyproject_check_import

export PYTHONPATH=%{buildroot}%{python3_sitearch}
# Upstream's configure_ANTs.sh copies data/ to ~/.antspy; the tests read the
# MNI and ch2 volumes from there. The slices resolve to the installed
# %%{_datadir}/antspyx copies, so point the patched lookup at the buildroot.
export HOME=$PWD/test-home
mkdir -p $HOME/.antspy
cp -p data/*.nii.gz $HOME/.antspy/
sed -i "s|^SYSTEM_DATA_DIRECTORY = .*|SYSTEM_DATA_DIRECTORY = '%{buildroot}%{_datadir}/antspyx'|" \
    %{buildroot}%{python3_sitearch}/ants/utils/get_ants_data.py

# 1. Real operations through the system libl_* libraries, with numbers checked.
cd /
%{python3} - <<'PYEOF'
import numpy as np, ants
fi = ants.image_read(ants.get_data('r16'))
mi = ants.image_read(ants.get_data('r64'))
assert fi.shape == (256, 256) and mi.shape == (256, 256), (fi.shape, mi.shape)

def mi_metric(a, b):
    return ants.image_mutual_information(a, b)

before = mi_metric(fi, mi)
reg = ants.registration(fi, mi, type_of_transform='SyN', random_seed=42)
after = mi_metric(fi, reg['warpedmovout'])
print(f"SyN r64->r16: MI {before:.4f} -> {after:.4f}")
# ANTs' MI is negative; more negative is better.
assert after < before - 0.1, (before, after)
assert len(reg['fwdtransforms']) == 2 and len(reg['invtransforms']) == 2

# Same seed, same answer (antsRegistration through libl_antsRegistration).
reg2 = ants.registration(fi, mi, type_of_transform='SyN', random_seed=42)
d = np.abs(reg['warpedmovout'].numpy() - reg2['warpedmovout'].numpy()).max()
print("repeat max abs diff:", d)
assert d < 1e-3, d

# apply_transforms (libl_antsApplyTransforms) reproduces warpedmovout.
w = ants.apply_transforms(fi, mi, transformlist=reg['fwdtransforms'])
d = np.abs(w.numpy() - reg['warpedmovout'].numpy()).max()
assert d < 1e-3, d

# Vector image through apply_transforms: the in-memory itk::VectorImage path
# from ANTs b53aad3 (the -devel backport). Each channel must match a scalar warp.
vec = ants.merge_channels([mi, mi * 2])
wvec = ants.apply_transforms(fi, vec, transformlist=reg['fwdtransforms'])
ch = ants.split_channels(wvec)
assert len(ch) == 2
assert np.abs(ch[0].numpy() - w.numpy()).max() < 1e-3
assert np.abs(ch[1].numpy() - 2 * w.numpy()).max() < 1e-2

# N4 (libl_N4BiasFieldCorrection): remove a synthetic multiplicative bias.
yy, xx = np.mgrid[0:256, 0:256] / 255.0
bias = ants.from_numpy((1.0 + 0.8 * xx).astype('float32'), spacing=fi.spacing,
                       origin=fi.origin, direction=fi.direction)
biased = fi * bias
mask = ants.get_mask(fi)
n4 = ants.n4_bias_field_correction(biased, mask=mask)
def cv_of_ratio(img):
    r = (img.numpy() / np.maximum(fi.numpy(), 1e-3))[mask.numpy() > 0]
    return r.std() / r.mean()
print(f"N4: ratio CV {cv_of_ratio(biased):.3f} -> {cv_of_ratio(n4):.3f}")
assert cv_of_ratio(n4) < 0.5 * cv_of_ratio(biased)

# Resampling (libl_ResampleImage) and Atropos segmentation (libl_Atropos).
rs = ants.resample_image(fi, (2, 2), use_voxels=False, interp_type=0)
assert rs.shape == (128, 128), rs.shape
seg = ants.atropos(a=fi, m='[0.2,1x1]', c='[2,0]', i='kmeans[3]', x=mask)
labels = np.unique(seg['segmentation'].numpy())
assert set(labels.astype(int)) == {0, 1, 2, 3}, labels
print("ANTsPy checks passed")
PYEOF
cd -

# 2. Upstream's unit tests (offline: all data is local, see above).
cd tests
%pytest -v -p no:cacheprovider
cd -

%files -n python3-%{pypi_name} -f %{pyproject_files}
%license LICENSE
%doc README.md
%{_datadir}/antspyx/

%changelog
* Fri Oct 16 2026 Morgan Hough <morgan.hough@gmail.com> - 0.6.3-2
- No PEP 639 License-File in the metadata: save_files -L, LICENSE listed by hand.

* Fri Oct 16 2026 Morgan Hough <morgan.hough@gmail.com> - 0.6.3-1
- Initial package, linked against system ANTs (ANTs-devel) and ITK.