# Upstream's last release, v2.5.1 (2021-05), is 64 commits behind master,
# which carries CMake modernisation and typo fixes and has been quiet since
# 2023-04; the snapshot is what upstream itself builds.
%global commit 84ba5fd7672ca7d08f9f60a95ef4b68f0c81a090
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%global snapdate 20230407

Name:           seg3d
Version:        2.5.1^%{snapdate}git%{shortcommit}
# Explicit, not %%autorelease -- that macro is inert in this COPR
# (ci/PROCEDURES.md golden rule 3).
Release:        1%{?dist}
Summary:        Interactive segmentation of 3D medical and microscopy volumes

# src/License.txt is MIT (SCI Institute); 1235 of the 1257 compiled sources
# carry the MIT text and 19 carry no header.
#
# Core/ITKLiveWire/itkLiveWireImageFunction.h is an ITK 3.x-era file
# ("Copyright (c) Insight Software Consortium ... See ITKCopyright.txt"),
# whose licence was BSD-3-Clause before ITK 4 moved to Apache-2.0.
#
# Application/Tools/Algorithm/fibheap.{h,cc} is John Boyer's 1996 Fibonacci
# heap from Dr. Dobb's Journal: "permission to use and distribute the
# software is granted provided that this copyright notice remains in the
# source and the author (John Boyer) is acknowledged". SPDX has no
# identifier for it and fedora-license-data does not classify it. Fine for
# the COPR; needs a fedora-license-data request before any Fedora submission
# (KNOWN-ISSUES). The same file already ships in InsightToolkit5 through the
# ITKGrowCut remote module.
#
# The bundled tinyxml and the empty googletest submodule are deleted in
# %%prep; the Superbuild (which would download Boost, ITK, Python, Qt
# helpers, TetGen ...) is not used.
License:        MIT AND BSD-3-Clause
URL:            https://github.com/SCIInstitute/Seg3D
Source0:        %{url}/archive/%{commit}/Seg3D-%{commit}.tar.gz
Source1:        seg3d.desktop
Source2:        seg3d.metainfo.xml
# %%check: build a test volume and count the voxels of Seg3D's exports.
Source3:        seg3d-volume-check.py
# %%check: the Seg3D side, run with --headless --python.
Source4:        seg3d-headless-check.py
# Build from src/ against system libraries (find_package instead of the
# Superbuild's config files), system tinyxml and GoogleTest, Boost compat
# defines, ITK IO factories linked, Implicit Model tool (TetGen) left out.
Patch0:         seg3d-system-libraries.patch
# Boost.Filesystem/Asio/Lambda/tribool changes up to Boost 1.90.
Patch1:         seg3d-boost-1.90.patch
# Embed the system Python 3 through PyConfig instead of a bundled 3.4.
Patch2:         seg3d-python3-embed.patch
# <stack> includes (GCC 16), HDF5 1.12+ API, teem's private header.
Patch3:         seg3d-build-fixes.patch

BuildRequires:  cmake
BuildRequires:  ninja-build
BuildRequires:  gcc-c++
BuildRequires:  boost-devel
BuildRequires:  python3-devel
BuildRequires:  zlib-ng-compat-devel
BuildRequires:  libpng-devel
BuildRequires:  sqlite-devel
BuildRequires:  teem-devel
BuildRequires:  glew-devel
BuildRequires:  mesa-libGLU-devel
BuildRequires:  freetype-devel
BuildRequires:  tinyxml-devel
BuildRequires:  libX11-devel
BuildRequires:  qt5-qtbase-devel
BuildRequires:  qt5-qtsvg-devel
BuildRequires:  gtest-devel
BuildRequires:  gmock-devel
BuildRequires:  InsightToolkit5-devel >= 5.4
# ITK's CMake config loads ITKVtkGlue -> find_package(VTK), whose transitive
# dependencies vtk-devel does not pull in itself (same list as c3d.spec).
BuildRequires:  hdf5-devel
BuildRequires:  eigen3-devel
BuildRequires:  qt6-qtdeclarative-devel
%if 0%{?fedora}
BuildRequires:  libminc-devel
%endif
BuildRequires:  desktop-file-utils
BuildRequires:  /usr/bin/appstream-util
# GUI smoke test in %%check (xvfb-run comes with the Xvfb package)
BuildRequires:  xorg-x11-server-Xvfb
BuildRequires:  mesa-dri-drivers

# ITK freezes sonames across releases while adding symbols, so rpm's soname
# dependencies cannot see a too-old ITK; floor on the version built against.
# The two-part expansion is required: ">= UNSET" is satisfied, so an undefined
# macro would make the floor vacuous, which the %%build guard catches.
Requires:       InsightToolkit5%{?_isa} >= %{?itk_ver}%{!?itk_ver:UNSET}
# itk(abi): ITK_LEGACY_REMOVE changes class layouts at unchanged sonames, so the itk_ver floor alone let a
# consumer built against the removed state install over the present one (python3-simpleitk -11 on ITK -23
# returned all-zero images). Equality on the legacy-state token; see InsightToolkit5.spec.
Requires:       itk(abi) = %{?itk_abi}%{!?itk_abi:UNSET}
# The viewer's text overlay opens /usr/share/fonts/gnu-free/FreeSerif.ttf by
# path (Core/TextRenderer/TextRenderer.cc) and logs an error without it.
Requires:       gnu-free-serif-fonts
Requires:       hicolor-icon-theme

%description
Seg3D is an interactive volume segmentation tool from the SCI Institute,
University of Utah. It works on layered data and mask volumes (MRI, CT,
microscopy stacks) with manual painting, polyline and speedline tools,
ITK filters for thresholding, region growing, level sets and smoothing,
image registration, an isosurface view, and an embedded Python console that
can script every action. It reads and writes NRRD, NIfTI, DICOM, MATLAB,
MRC, TIFF/PNG stacks and the other formats ITK supports.

This build leaves out the Implicit Model tool, which needs TetGen
(AGPL-3.0-or-later). The large-volume converter is installed as
Seg3D2-CreateLargeVolume.

%prep
%autosetup -n Seg3D-%{commit} -p1
rm -r src/ThirdParty/tinyxml src/ThirdParty/submodules/googletest Superbuild

%build
test -n "%{?itk_ver}" || { echo "ERROR: itk_ver undefined - needs InsightToolkit5-devel's macros.itk" >&2; exit 1; }
test -n "%{?itk_abi}" || { echo "ERROR: itk_abi undefined - needs InsightToolkit5-devel >= 5.4.7-24 (macros.itk)" >&2; exit 1; }
# -fpermissive: GCC 16 rejects a few pre-C++17 idioms in the tree.
# -DNDEBUG: upstream builds Release; without it the Python start-up and the
# log streamer print debug output to stderr.
export CXXFLAGS="%{build_cxxflags} -fpermissive -DNDEBUG"
# SEG3D_BITS=64 selects the 64-bit code paths (SCI_64BITS); the Superbuild
# sets it from the pointer size, which is 64 on every Fedora architecture.
%cmake -S src -G Ninja \
    -DCMAKE_CXX_STANDARD=17 \
    -DSEG3D_BITS=64 \
    -DSEG3D_BUILD_INTERFACE=ON \
    -DBUILD_WITH_PYTHON=ON \
    -DBUILD_LARGE_VOLUME_TOOLS=ON \
    -DBUILD_MOSAIC_TOOLS=OFF \
    -DBUILD_TESTING=ON
%cmake_build

%install
# Upstream has no Linux install rules (only CPack bundles for macOS and
# Windows); resources are compiled in through Qt's resource system.
install -Dpm 0755 %{__cmake_builddir}/Seg3D2 %{buildroot}%{_bindir}/Seg3D2
install -Dpm 0755 %{__cmake_builddir}/CreateLargeVolume \
    %{buildroot}%{_bindir}/Seg3D2-CreateLargeVolume
desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE1}
install -Dpm 0644 src/Resources/Icons/seg3d2_128.png \
    %{buildroot}%{_datadir}/icons/hicolor/128x128/apps/seg3d.png
install -Dpm 0644 src/Resources/Icons/seg3d2_256.png \
    %{buildroot}%{_datadir}/icons/hicolor/256x256/apps/seg3d.png
install -Dpm 0644 %{SOURCE2} %{buildroot}%{_metainfodir}/seg3d.metainfo.xml

%check
desktop-file-validate %{buildroot}%{_datadir}/applications/seg3d.desktop
appstream-util validate-relax --nonet %{buildroot}%{_metainfodir}/seg3d.metainfo.xml

export HOME=$(mktemp -d)
# Upstream's unit tests (53 cases in 7 suites). Application_Socket_Tests
# initialises the Python interpreter once per test case, and Python 3.14
# aborts on a second PyImport_AppendInittab in one process, so its two cases
# run as separate processes.
%ctest --exclude-regex Application_Socket_Tests
for t in StartSocket ConnectToSocket; do
    %{__cmake_builddir}/Application_Socket_Tests --gtest_filter=ActionSocketTests.$t
done

# Functional test of the installed binary, headless and in the GUI under
# Xvfb: read the same volume through teem (NRRD) and ITK (MetaImage),
# threshold both, grow an ITK ConfidenceConnected region, export NRRD masks
# and count their voxels. A broken ITK IO factory or ITK ABI shows up as an
# empty mask, not a crash, so exact counts are the oracle.
exe=%{buildroot}%{_bindir}/Seg3D2
for mode in headless gui; do
    out=$(mktemp -d)
    %{python3} -I %{SOURCE3} make $out/in
    if [ $mode = headless ]; then
        run="$exe --headless"
    else
        run="xvfb-run -a -s '-screen 0 1280x1024x24' $exe --nosplash"
    fi
    SEG3D_CHECK_IN=$out/in SEG3D_CHECK_OUT=$out \
        timeout 300 sh -c "$run --python=%{SOURCE4}" | tee $out/log
    grep -q '^seg3d-check: exported' $out/log
    %{python3} -I %{SOURCE3} count $out/both/*.nrrd 4351
    %{python3} -I %{SOURCE3} count $out/ball/*.nrrd 3071
    %{python3} -I %{SOURCE3} count $out/itkball/*.nrrd 3071
    %{python3} -I %{SOURCE3} count $out/grown/*.nrrd 3071
done

%files
%license src/License.txt
%doc README.md src/ReleaseNotes.txt
%{_bindir}/Seg3D2
%{_bindir}/Seg3D2-CreateLargeVolume
%{_datadir}/applications/seg3d.desktop
%{_datadir}/icons/hicolor/128x128/apps/seg3d.png
%{_datadir}/icons/hicolor/256x256/apps/seg3d.png
%{_metainfodir}/seg3d.metainfo.xml

%changelog
* Thu Oct 08 2026 Morgan Hough <morgan.hough@gmail.com> - 2.5.1^20230407git84ba5fd-1
- Initial package: master 84ba5fd built from src/ against system libraries
  (ITK under itk(abi), Boost 1.90, Python 3.14, Qt 5, teem, tinyxml)
- Implicit Model tool left out (TetGen is AGPL-3.0-or-later)
- %%check: upstream unit tests and a headless + Xvfb GUI pipeline whose
  exported masks must have exact voxel counts