# SlicerMONAIAuto3DSeg: automatic segmentation in 3D Slicer with MONAI Auto3DSeg
# (SegResNet) models -- whole body and abdominal CT organs, vertebrae, mediastinal
# anatomy, whole head MRI, brain tumours (BraTS), prostate, intracranial haemorrhage
# and more (33 models in Resources/Models.json). Inference runs in a separate
# PythonSlicer process.
#
# PURE-SCRIPTED: nothing to compile. Upstream pip-installs MONAI and its extras and
# gets PyTorch through the PyTorch extension; here they are RPMs (Patch0). The model
# weights are not packaged: the module downloads the chosen model from the project's
# GitHub release into ~/.MONAIAuto3DSeg and shows its licence (most are CC BY 4.0).

%global commit      9cdf2df4e8b3a5351ad11a3f934b0c13ffb15cca
%global shortcommit %(c=%{commit}; echo ${c:0:8})
%global snapdate    20260319

%global slicer_inst   %{_prefix}/lib/slicer
%global slicer_subdir Slicer-5.12
%global qtsm          %{slicer_inst}/lib/%{slicer_subdir}/qt-scripted-modules

Name:           3dslicer-monaiauto3dseg
Version:        0
Release:        0.1.%{snapdate}git%{shortcommit}%{?dist}
Summary:        MONAI Auto3DSeg automatic segmentation for 3D Slicer

License:        MIT
URL:            https://github.com/lassoan/SlicerMONAIAuto3DSeg
Source0:        %{url}/archive/%{commit}/SlicerMONAIAuto3DSeg-%{shortcommit}.tar.gz
# - SlicerPythonDependencies.setupPythonRequirements(): check that MONAI (>= 1.3) and
#   the extras inference uses import, with a dnf hint, instead of
#   pip_install("monai[fire,pyyaml,nibabel,pynrrd,psutil,tensorboard,skimage,itk,tqdm]>=1.3"),
#   which upstream runs every time (tensorboard is training-only).
# - Inference-server toggle: check fastapi/uvicorn/python-multipart/slowapi/psutil
#   instead of pip-installing them; slowapi is not packaged, so the server reports it.
Patch0:         3dslicer-monaiauto3dseg-fedora-packages.patch

BuildArch:      noarch

# Inference runs in a child process found as shutil.which("PythonSlicer"), which
# 3dslicer ships from 5.12.4-14.
Requires:       3dslicer >= 5.12.4-14
# EXTENSION_DEPENDS PyTorch: setupPythonRequirements() uses PyTorchUtils.
Requires:       3dslicer-pytorch
Requires:       python3-torch
Requires:       python3-monai >= 1.3
Requires:       python3-fire
Requires:       python3-pyyaml
Requires:       python3-nibabel
Requires:       python3-pynrrd
Requires:       python3-psutil
Requires:       python3-scikit-image
Requires:       python3-itk
Requires:       python3-tqdm
Requires:       python3-packaging
Requires:       python3-requests
Requires:       python3-numpy

%description
SlicerMONAIAuto3DSeg segments medical images automatically with MONAI Auto3DSeg
models: CT organs of the whole body and abdomen, vertebrae, mediastinal
anatomy, whole-head MRI, brain tumours, prostate MRI and more. Inference runs
in a separate process, so Slicer stays responsive.

MONAI and PyTorch come from Fedora packages; Fedora's PyTorch has no CUDA
support, so inference runs on the CPU, or on AMD GPUs through ROCm. Models are
downloaded on first use into ~/.MONAIAuto3DSeg; the module shows each model's
licence.

%prep
%autosetup -n SlicerMONAIAuto3DSeg-%{commit} -p1

%build
# Pure-scripted: nothing to compile.

%install
# Install exactly what MONAIAuto3DSeg/CMakeLists.txt lists, at the paths
# slicerMacroBuildScriptedModule uses.
_dir=MONAIAuto3DSeg; _mod=MONAIAuto3DSeg; _n=0
for _f in $(sed -n '/^set(MODULE_PYTHON_\(SCRIPTS\|RESOURCES\)$/,/^  )$/p' $_dir/CMakeLists.txt \
            | grep -vE '^set\(|^  \)$' | sed -e 's/^ *//' -e "s/\${MODULE_NAME}/$_mod/g"); do
    test -f "$_dir/$_f" || { echo "ERROR: $_mod lists $_f, which is missing" >&2; exit 1; }
    install -Dpm0644 "$_dir/$_f" "%{buildroot}%{qtsm}/$_f"
    _n=$((_n + 1))
done
test "$_n" -eq 24 || { echo "ERROR: installed $_n $_mod files, expected 24 (8 scripts, 16 resources)" >&2; exit 1; }

( cd %{buildroot} && find . \( -type f -o -type l \) | sed 's|^\.||' ) > %{_builddir}/monaiauto3dseg.files

%files -f %{_builddir}/monaiauto3dseg.files
%license LICENSE
%doc README.md UsingStandardTerminology.md

%changelog
* Sat Oct 10 2026 Morgan Hough <morgan.hough@gmail.com> - 0-0.1.20260319git9cdf2df4
- Initial package. SlicerMONAIAuto3DSeg on python3-monai / python3-torch; no pip
  (Patch0).