# Newest tag is release-1.0.20; master has moved past it and is what the ACES
# tree builds from, so package the tip as the other MNI components here do.
# configure.ac still says 1.0.4.
%global commit  ef9e6cb00bfbbd98f5f32114e6c8e2f86517dfb2
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%global date    20190627

Name:           inormalize
Version:        1.0.20
Release:        1.%{date}git%{shortcommit}%{?dist}
Summary:        Intensity normalization for MINC volumes

# COPYING: the classic MNI/BIC permissive notice, Alex Zijdenbos 2006-2007.
# docs/civet-licensing.md (tier 1).
License:        HPND
URL:            https://github.com/aces/inormalize
Source0:        %{url}/archive/%{commit}/%{name}-%{shortcommit}.tar.gz
# m4/ is a git submodule (BIC-MNI/mni-acmacros) and absent from the archive.
Source1:        https://github.com/BIC-MNI/mni-acmacros/archive/master.tar.gz#/mni-acmacros.tar.gz
# Maps the pre-VIO_ volume_io spellings this code uses onto current libminc.
Source2:        mni-volume-io-compat.h
# defined(@array), removed in Perl 5.22. Same construct as N3's drivers; see
# docs/upstream/mni-perl-defined-array.md
Patch0:         inormalize-perl-defined-array.patch

BuildRequires:  autoconf
BuildRequires:  automake
BuildRequires:  gcc
BuildRequires:  gcc-c++
BuildRequires:  libtool
BuildRequires:  make
BuildRequires:  perl-interpreter
# %%check syntax-checks the drivers, which use these at compile time.
BuildRequires:  perl-MNI
BuildRequires:  perl(Getopt::Tabular)
BuildRequires:  EBTKS-devel
BuildRequires:  libminc-devel
BuildRequires:  netcdf-devel
BuildRequires:  zlib-devel

# nu_correct_norm, normalize_mri, lgmask and headmask are MNI::Startup scripts
# that parse options with Getopt::Tabular and drive the MINC tools.
Requires:       perl-MNI
Requires:       perl(Getopt::Tabular)
Requires:       minc-tools

%description
inormalize normalizes the intensity of a MINC volume, by one of several
methods: matching a ratio, a median, or the peak of the intensity histogram,
optionally within a mask. It is used throughout the MNI/BIC pipelines, and by
CIVET, to put volumes on a common intensity scale before further processing.

The package also provides nu_correct_norm, which pairs the normalization with
N3's non-uniformity correction, and the lgmask and headmask helpers.

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

# Supply the mni-acmacros submodule that the tarball cannot carry.
mkdir -p m4
tar -xf %{SOURCE1} --strip-components=1 -C m4
test -f m4/smr_WITH_BUILD_PATH.m4

%build
autoreconf -ifv -I m4

# Fedora's libminc names its volume_io library libminc_io, not libvolume_io2.
sed -i 's/volume_io2/minc_io/g' configure
grep -q 'minc_io' configure

cp %{SOURCE2} compat_minc.h

export CXXFLAGS="%{optflags} -std=gnu++17 -fpermissive -I%{_includedir}/libminc \
    -include $(pwd)/compat_minc.h"
# The MNI configure probes are pre-C99 (mni_REQUIRE_LIB(z) assigns a function
# pointer to an int, others call undeclared functions); GCC 14+ makes those hard
# errors, so the probes fail to compile and configure reports the libraries as
# missing. Demote them, as bicpl and N3 do.
export CFLAGS="%{optflags} -std=gnu17 -I%{_includedir}/libminc \
    -Wno-error=implicit-function-declaration -Wno-error=implicit-int \
    -Wno-error=incompatible-pointer-types -Wno-error=int-conversion \
    -include $(pwd)/compat_minc.h"

%configure \
    --with-minc2 \
    --with-build-path=%{_prefix} \
    LIBS="-lminc_io -lminc2 -lnetcdf -lhdf5 -lz -lm"
%make_build

%install
%make_install
find %{buildroot} -name '*.la' -delete

%check
# No test suite upstream. Check that the binary runs and that each Perl driver
# at least compiles -- they are generated by sed from .in files, so a broken
# substitution would otherwise ship silently.
./inormalize -help 2>&1 | grep -qi 'usage\|inormalize'
for f in nu_correct_norm normalize_mri lgmask headmask; do
    %{__perl} -c "$f"
done

%files
%license COPYING
%doc AUTHORS ChangeLog NEWS README
%{_bindir}/inormalize
%{_bindir}/nu_correct_norm
%{_bindir}/normalize_mri
%{_bindir}/lgmask
%{_bindir}/headmask

%changelog
* Thu Sep 24 2026 Morgan Hough <morgan.hough@gmail.com> - 1.0.20-1.20190627gitef9e6cb
- Initial package, from the tip of upstream master. CIVET/MNI tier 1
  (docs/civet-licensing.md); the fourth of the eight permissive components.