# FastSurfer: deep-learning whole-brain segmentation (FastSurferVINN), plus the
# CerebNet (cerebellum), HypVINN (hypothalamus) and FastSurfer-CC (corpus callosum)
# networks, from Deep-MI. This package is the Python code and the trained networks.
#
# Not here: recon-surf, FastSurfer's surface pipeline. It runs FreeSurfer 8.2 binaries
# and needs a FreeSurfer licence key, so it belongs with freesurfer8 in
# neurofedora-nonfree. The recon_surf Python package is still installed (it is in
# upstream's wheel), but nothing here can run it without FreeSurfer.
#
# The trained checkpoints are not in the source tarball; upstream downloads them on
# first use. They are on Zenodo under free licences (Apache-2.0: FastSurferVINN;
# CC-BY-4.0: CerebNet, HypVINN), so they ship here as noarch data
# subpackages under %%{_datadir}/fastsurfer/checkpoints, and Patch0 makes the code
# look there, then in the per-user cache, instead of beside its own sources.

%global pypi_name fastsurfer
%global ckpt_dir  %{_datadir}/fastsurfer

Name:           python-%{pypi_name}
Version:        2.6.0
Release:        1%{?dist}
Summary:        Deep-learning neuroimaging segmentation (FastSurferVINN, CerebNet, HypVINN)

License:        Apache-2.0
URL:            https://github.com/Deep-MI/FastSurfer
Source0:        %{url}/archive/v%{version}/FastSurfer-%{version}.tar.gz
# FastSurferVINN, Zenodo record 10390573 (v2.0.0), Apache-2.0
Source10:       https://zenodo.org/records/10390573/files/aparc_vinn_axial_v2.0.0.pkl
Source11:       https://zenodo.org/records/10390573/files/aparc_vinn_coronal_v2.0.0.pkl
Source12:       https://zenodo.org/records/10390573/files/aparc_vinn_sagittal_v2.0.0.pkl
# CerebNet, Zenodo record 10390742 (v1.0.0), CC-BY-4.0
Source13:       https://zenodo.org/records/10390742/files/CerebNet_axial_v1.0.0.pkl
Source14:       https://zenodo.org/records/10390742/files/CerebNet_coronal_v1.0.0.pkl
Source15:       https://zenodo.org/records/10390742/files/CerebNet_sagittal_v1.0.0.pkl
# HypVINN, Zenodo record 11184216 (v1.1.0), CC-BY-4.0
Source16:       https://zenodo.org/records/11184216/files/HypVINN_axial_v1.1.0.pkl
Source17:       https://zenodo.org/records/11184216/files/HypVINN_coronal_v1.1.0.pkl
Source18:       https://zenodo.org/records/11184216/files/HypVINN_sagittal_v1.1.0.pkl
# FastSurfer-CC's checkpoints (Zenodo 17141933, Apache-2.0) are not shipped yet: the
# CC code needs meshpy and neuroreg, which are not packaged.
# Zenodo's MD5s for Source10-18, checked in %%prep.
Source30:       python-fastsurfer-checkpoints.md5

# Resolve "checkpoints/..." through one helper: FASTSURFER_CHECKPOINT_ROOT (this
# package sets its default to %%{ckpt_dir} in %%prep), then the per-user cache
# $XDG_CACHE_HOME/fastsurfer, where missing checkpoints are also downloaded. Upstream
# resolved them against the source tree, which is site-packages once installed.
Patch0:         python-fastsurfer-checkpoint-root.patch

BuildArch:      noarch
BuildRequires:  python3-devel
BuildRequires:  python3dist(setuptools) >= 61
# %%check imports the segmentation path.
BuildRequires:  python3dist(torch)
BuildRequires:  python3dist(torchvision)
BuildRequires:  python3dist(numpy)
BuildRequires:  python3dist(nibabel)
BuildRequires:  python3dist(scipy)
BuildRequires:  python3dist(scikit-image)
BuildRequires:  python3dist(h5py)
BuildRequires:  python3dist(pyyaml)
BuildRequires:  python3dist(yacs)
BuildRequires:  python3dist(simpleitk)
BuildRequires:  python3dist(pandas)
BuildRequires:  python3dist(matplotlib)
BuildRequires:  python3dist(requests)
BuildRequires:  python3dist(tqdm)
BuildRequires:  python3dist(scikit-learn)
BuildRequires:  python3dist(monai)
BuildRequires:  python3dist(lapy)

%global _description %{expand:
FastSurfer is a deep-learning pipeline for brain MRI. FastSurferVINN segments a
T1-weighted image into the DKT cortical parcellation and subcortical structures
in minutes on a CPU, and seconds on a GPU. CerebNet adds a cerebellum
sub-segmentation, HypVINN a hypothalamus sub-segmentation, and FastSurfer-CC
corpus callosum segmentation and morphometry.}

%description %_description

%package -n     python3-%{pypi_name}
Summary:        %{summary}
# The networks, installed by default but separable: without them, FastSurfer
# downloads the checkpoints it needs into ~/.cache/fastsurfer on first use.
Recommends:     %{name}-checkpoints-vinn = %{version}-%{release}
Recommends:     %{name}-checkpoints-cerebnet = %{version}-%{release}
Recommends:     %{name}-checkpoints-hypvinn = %{version}-%{release}

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

The fastsurfer-seg command runs the FastSurferVINN segmentation
(FastSurferCNN/run_prediction.py). FastSurfer-CC (corpus callosum) also needs
meshpy, neuroreg and pyrr, and training needs tensorboard and torchio; none of
them is packaged yet, and neither are the FastSurfer-CC checkpoints. recon-surf (surfaces) needs FreeSurfer and is not part of this
package.

%package        checkpoints-vinn
Summary:        FastSurferVINN trained networks (whole-brain segmentation)
License:        Apache-2.0
Requires:       python3-%{pypi_name} = %{version}-%{release}

%description    checkpoints-vinn
The axial, coronal and sagittal FastSurferVINN checkpoints (v2.0.0, Zenodo
record 10390573) that FastSurfer's default segmentation uses.

%package        checkpoints-cerebnet
Summary:        CerebNet trained networks (cerebellum sub-segmentation)
License:        CC-BY-4.0
Requires:       python3-%{pypi_name} = %{version}-%{release}

%description    checkpoints-cerebnet
The axial, coronal and sagittal CerebNet checkpoints (v1.0.0, Zenodo record
10390742). Henschel et al., NeuroImage 2022.

%package        checkpoints-hypvinn
Summary:        HypVINN trained networks (hypothalamus sub-segmentation)
License:        CC-BY-4.0
Requires:       python3-%{pypi_name} = %{version}-%{release}

%description    checkpoints-hypvinn
The axial, coronal and sagittal HypVINN checkpoints (v1.1.0, Zenodo record
11184216). Estrada et al., Imaging Neuroscience 2023.

%prep
%autosetup -p1 -n FastSurfer-%{version}

# The checkpoint files are what Zenodo lists for each record.
(cd %{_sourcedir} && md5sum --quiet -c %{SOURCE30})

# Default checkpoint root: this package's data directory.
sed -i 's|os.environ.get("FASTSURFER_CHECKPOINT_ROOT", str(FASTSURFER_ROOT))|os.environ.get("FASTSURFER_CHECKPOINT_ROOT", "%{ckpt_dir}")|' \
    FastSurferCNN/utils/parser_defaults.py
grep -q '"FASTSURFER_CHECKPOINT_ROOT", "%{ckpt_dir}"' FastSurferCNN/utils/parser_defaults.py \
    || { echo "ERROR: checkpoint root default not set" >&2; exit 1; }

# Requirements, to what Fedora has and the installed code needs:
# - torch==2.14.* and torchvision>=0.29,<0.30 pin upstream's container build, not an
#   API (2.4.x required torch>=2.0.1; there is no runtime version check). Fedora 44
#   has torch 2.9.1, which runs the full segmentation (see %%changelog).
# - libigl (recon-surf's cortical ribbon, recon_surf/volmask.py), meshpy, pyrr
#   (FastSurfer-CC), neuroreg (registration, eTIV) and tensorboard, torchio (training)
#   are not packaged; the segmentation path does not import them.
# - pip is a packaging-tool requirement of upstream's environment, not of the code.
%{python3} - <<'EOF'
import re
p = "pyproject.toml"
s = open(p).read()
drop = ("libigl", "meshpy", "neuroreg", "pyrr", "tensorboard", "torchio", "pip")
relax = {"torch": "torch", "torchvision": "torchvision"}
out, done = [], set()
for line in s.splitlines(keepends=True):
    m = re.match(r"^(\s*)'([A-Za-z0-9_.-]+)[^']*',.*$", line)
    if m and m.group(2) in drop:
        done.add(m.group(2))
        continue
    if m and m.group(2) in relax:
        line = f"{m.group(1)}'{relax[m.group(2)]}',\n"
        done.add(m.group(2))
    out.append(line)
missing = (set(drop) | set(relax)) - done
if missing:
    raise SystemExit(f"pyproject.toml: requirement lines not found: {sorted(missing)}")
open(p, "w").write("".join(out))
print("requirements: dropped", sorted(drop), "unpinned", sorted(relax))
EOF

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files FastSurferCNN CerebNet CorpusCallosum HypVINN recon_surf

install -d %{buildroot}%{ckpt_dir}/checkpoints
for s in %{SOURCE10} %{SOURCE11} %{SOURCE12} %{SOURCE13} %{SOURCE14} %{SOURCE15} \
         %{SOURCE16} %{SOURCE17} %{SOURCE18}; do
    install -p -m 0644 "$s" %{buildroot}%{ckpt_dir}/checkpoints/
done

# Segmentation entry point; upstream calls the script by path from run_fastsurfer.sh.
install -d %{buildroot}%{_bindir}
cat > %{buildroot}%{_bindir}/fastsurfer-seg <<'EOF'
#!/bin/sh
# FastSurferVINN segmentation (FastSurferCNN/run_prediction.py). See --help.
exec /usr/bin/python3 -m FastSurferCNN.run_prediction "$@"
EOF
chmod 0755 %{buildroot}%{_bindir}/fastsurfer-seg

%check
# Every module imports except these, measured: FastSurfer-CC's five need meshpy or
# neuroreg, train/run_model need tensorboard, and recon_surf is FreeSurfer-pipeline
# scripts importing each other by flat name.
%pyproject_check_import -e 'recon_surf*' -e FastSurferCNN.train -e FastSurferCNN.run_model -e CorpusCallosum.cc_visualization -e CorpusCallosum.data.fsaverage_cc_template -e CorpusCallosum.fastsurfer_cc -e CorpusCallosum.registration.midsagittal_plane_alignment -e 'CorpusCallosum.shape*'
# Checkpoint paths resolve to the system directory, then the user cache.
export PYTHONPATH=%{buildroot}%{python3_sitelib}
FASTSURFER_CHECKPOINT_ROOT=%{buildroot}%{ckpt_dir} XDG_CACHE_HOME=/nonexistent %{python3} - <<'EOF'
from pathlib import Path
from FastSurferCNN.utils.parser_defaults import resolve_fastsurfer_path
from FastSurferCNN.utils.checkpoint import load_checkpoint_config_defaults, get_config_file
ckpts = load_checkpoint_config_defaults("checkpoint", filename=get_config_file("FastSurferCNN"))
for plane, rel in ckpts.items():
    p = resolve_fastsurfer_path(rel)
    assert p.is_file() and "%{ckpt_dir}" in str(p), (plane, p)
missing = resolve_fastsurfer_path("checkpoints/not-shipped.pkl")
assert missing == Path("/nonexistent/fastsurfer/checkpoints/not-shipped.pkl"), missing
print("checkpoint resolution OK:", sorted(ckpts))
EOF
%{buildroot}%{_bindir}/fastsurfer-seg --help >/dev/null

%files -n python3-%{pypi_name} -f %{pyproject_files}
%license LICENSE
%doc README.md notice.txt
%{_bindir}/fastsurfer-seg
%dir %{ckpt_dir}
%dir %{ckpt_dir}/checkpoints

%files checkpoints-vinn
%{ckpt_dir}/checkpoints/aparc_vinn_*_v2.0.0.pkl

%files checkpoints-cerebnet
%{ckpt_dir}/checkpoints/CerebNet_*_v1.0.0.pkl

%files checkpoints-hypvinn
%{ckpt_dir}/checkpoints/HypVINN_*_v1.1.0.pkl


%changelog
* Sat Oct 10 2026 Morgan Hough <morgan.hough@gmail.com> - 2.6.0-1
- Initial package. FastSurfer 2.6.0 code plus three trained networks (FastSurferVINN,
  CerebNet, HypVINN) as data subpackages. FastSurfer-CC waits for meshpy and neuroreg;
  recon-surf (needs FreeSurfer) is for neurofedora-nonfree.
- Measured before packaging, f44 x86_64, Fedora torch 2.9.1 (CPU), 8 threads, an HBN
  T1w: full FastSurferVINN segmentation in 22 min 55 s, 3.9 GB peak RSS; Dice against
  the same subject's FreeSurfer 6 aparc.DKTatlas+aseg: 0.915 mean over 21 subcortical,
  ventricle, cerebellar and white-matter labels, 0.892 mean over 62 DKT cortical
  parcels.