# SlicerRadiomics: the 3D Slicer interface to PyRadiomics. A scripted module
# (Radiomics, under Informatics) computes radiomics features of segments or label
# maps into a table; a Python CLI (SlicerRadiomicsCLI) runs the pyradiomics
# command line on files.
#
# PURE-SCRIPTED: nothing to compile. Upstream's superbuild pip-installs pyradiomics
# (146e3bd0) into the extension; here it is python3-pyradiomics.

%global commit      063a9ded6e9a8a5af3f0dea209321e9e30237c0d
%global shortcommit %(c=%{commit}; echo ${c:0:8})
%global snapdate    20260620

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

Name:           3dslicer-radiomics
Version:        0
Release:        0.1.%{snapdate}git%{shortcommit}%{?dist}
Summary:        Radiomics feature extraction (PyRadiomics) for 3D Slicer

License:        BSD-3-Clause
URL:            https://github.com/AIM-Harvard/SlicerRadiomics
Source0:        %{url}/archive/%{commit}/SlicerRadiomics-%{shortcommit}.tar.gz
# Read the label map with sitkUtils.PullVolumeFromSlicer (numpy-based, how Slicer 5.12's
# own sitkUtils pulls volumes) instead of sitk.ReadImage on a "slicer:<scene>#<id>"
# address, which needs Slicer's MRMLIDImageIO ITK plugin: it is not built here
# (lib/Slicer-5.12/ITKFactories does not exist), so every label-map extraction failed
# with 'The file "slicer:0x...#vtkMRMLLabelMapVolumeNode1" does not exist.'
Patch0:         3dslicer-radiomics-pull-volume.patch

BuildArch:      noarch

Requires:       3dslicer
Requires:       python3-pyradiomics
# Imported by the module (SlicerRadiomics.py).
Requires:       python3-pywt
Requires:       python3-six
Requires:       python3-dateutil
Requires:       python3-simpleitk
Requires:       python3-numpy

%description
SlicerRadiomics provides a 3D Slicer interface to PyRadiomics, an open-source
Python package for extracting radiomics features from medical images: shape,
first-order statistics and texture features, on the original image and on
filtered images. Features of segments or label maps are written to a table. A
command-line module runs PyRadiomics on image and mask files.

%prep
%autosetup -n SlicerRadiomics-%{commit} -p1
# The CLI's "#!/usr/bin/env python-real" (Slicer's superbuild interpreter) would make
# rpm generate an unsatisfiable Requires: /usr/bin/python-real; Slicer runs Python CLIs
# with the system interpreter here (see 3dslicer.spec).
sed -i '1s|^#!/usr/bin/env python-real$|#!/usr/bin/python3|' SlicerRadiomicsCLI/SlicerRadiomicsCLI.py
head -1 SlicerRadiomicsCLI/SlicerRadiomicsCLI.py | grep -qx '#!/usr/bin/python3' \
    || { echo "ERROR: CLI shebang not rewritten" >&2; exit 1; }

%build
# Pure-scripted: nothing to compile.

%install
# The scripted module: exactly what SlicerRadiomics/CMakeLists.txt lists.
_mod=SlicerRadiomics; _n=0
for _f in $(sed -n '/^set(MODULE_PYTHON_\(SCRIPTS\|RESOURCES\)$/,/^  )$/p' $_mod/CMakeLists.txt \
            | grep -vE '^set\(|^  \)$' | sed -e 's/^ *//' -e "s/\${MODULE_NAME}/$_mod/g"); do
    test -f "$_mod/$_f" || { echo "ERROR: $_mod lists $_f, which is missing" >&2; exit 1; }
    install -Dpm0644 "$_mod/$_f" "%{buildroot}%{qtsm}/$_f"
    _n=$((_n + 1))
done
test "$_n" -eq 2 || { echo "ERROR: installed $_n $_mod files, expected 2" >&2; exit 1; }
# The CLI: script + XML descriptor into cli-modules (SlicerRadiomicsAddCLI's rules).
install -Dpm0644 SlicerRadiomicsCLI/SlicerRadiomicsCLI.xml %{buildroot}%{climod}/SlicerRadiomicsCLI.xml
install -Dpm0755 SlicerRadiomicsCLI/SlicerRadiomicsCLI.py  %{buildroot}%{climod}/SlicerRadiomicsCLI.py

%files
%license LICENSE.txt
%doc README.md USAGE.md
%{qtsm}/SlicerRadiomics.py
%{qtsm}/Resources/Icons/SlicerRadiomics.png
%{climod}/SlicerRadiomicsCLI.py
%{climod}/SlicerRadiomicsCLI.xml

%changelog
* Sat Oct 10 2026 Morgan Hough <morgan.hough@gmail.com> - 0-0.1.20260620git063a9ded
- Initial package. SlicerRadiomics (module + Python CLI) on python3-pyradiomics.
- Patch0: read label maps with sitkUtils.PullVolumeFromSlicer, not a slicer: address.