# Newest tag is release-1.6.80; master has moved past it and is what the ACES
# tree builds from. configure.ac still says 1.6.7.
%global commit  166303dcfd95f83c54a1fdcdab1a63e6714f349b
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%global date    20120308

Name:           conglomerate
Version:        1.6.80
Release:        1.%{date}git%{shortcommit}%{?dist}
Summary:        MNI/BIC tools for MINC volumes and geometric objects

# COPYING: the classic MNI/BIC permissive notice, David MacDonald 1993-1995.
# docs/civet-licensing.md (tier 1).
License:        HPND
URL:            https://github.com/aces/conglomerate
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

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

# The driver scripts are MNI::Startup Perl and shell, and run the MINC tools.
Requires:       bicpl
Requires:       minc-tools
Requires:       perl-MNI
Requires:       perl(Getopt::Tabular)

%description
conglomerate is the MNI/BIC collection of command line tools for MINC volumes
and for the .obj geometric objects the surface pipelines produce: volume
arithmetic and statistics, tag and label handling, surface measurement,
resampling, smoothing and format conversion.

It provides 132 programs, among them compute_icbm_vols, which CIVET uses to
report tissue volumes, and the surface tools the cortical thickness steps
depend on.

%prep
%autosetup -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
# configure.ac has AC_PROG_CXX commented out (line 15) while Makefile.am builds
# two C++ programs, mincdefrag and mincskel. Current automake refuses that:
#   Makefile.am: error: C++ source seen but 'CXX' is undefined
# Older automake let it slide by falling back to the C compiler.
sed -i 's/^dnl AC_PROG_CXX$/AC_PROG_CXX/' configure.ac
grep -q '^AC_PROG_CXX$' configure.ac

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

# 239 sources include <volume_io/internal_volume_io.h>. That header was part of
# volume_io's internals and libminc 2.x does not install it; everything those
# files need is in the public <volume_io.h>. Provide it as a one-line shim on
# the include path rather than editing 239 files -- and so the diff stays
# reviewable if upstream ever adopts it.
mkdir -p compat/volume_io
cat > compat/volume_io/internal_volume_io.h <<'SHIM'
/* libminc 2.x installs no volume_io/internal_volume_io.h; the public header
   carries the same declarations for every use in this package. */
#ifndef MNI_COMPAT_INTERNAL_VOLUME_IO_H
#define MNI_COMPAT_INTERNAL_VOLUME_IO_H
#include <volume_io.h>
#endif
SHIM

# Mostly C, and it indexes coordinates as X, Y, Z, so the axis macros are
# wanted here. They are opt-in because they rewrite any identifier of those
# names; the C++ files below are compiled without them for that reason.
export CFLAGS="%{optflags} -std=gnu17 -I$(pwd)/compat -I%{_includedir}/libminc \
    -Wno-error=implicit-function-declaration -Wno-error=implicit-int \
    -Wno-error=incompatible-pointer-types -Wno-error=int-conversion \
    -include $(pwd)/compat_minc.h -DMNI_COMPAT_AXIS_MACROS"
export CXXFLAGS="%{optflags} -std=gnu++17 -fpermissive -I$(pwd)/compat -I%{_includedir}/libminc \
    -include $(pwd)/compat_minc.h"

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

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

%check
# No test suite upstream. Assert the full program set is present -- with 132
# binaries a missing one is easy to miss -- and syntax-check the Perl drivers,
# which are generated by sed and would otherwise ship broken and silent.
n=$(ls -1 %{buildroot}%{_bindir} | wc -l)
test "$n" -eq 141 || { echo "expected 141 programs in bindir, found $n"; exit 1; }
echo "141 programs installed"
for f in %{buildroot}%{_bindir}/*; do
    # `grep -q ... && perl -c` would abort the whole script under set -e the
    # first time grep does not match, i.e. at the first compiled binary.
    if head -1 "$f" | grep -q '^#!.*perl'; then
        %{__perl} -c "$f"
    fi
done

%files
%license COPYING
%doc AUTHORS ChangeLog NEWS README TODO
%{_bindir}/add_labels
%{_bindir}/apply_sphere_transform
%{_bindir}/autocrop_volume
%{_bindir}/average_voxels
%{_bindir}/blur_surface
%{_bindir}/box_filter_volume
%{_bindir}/box_filter_volume_nd
%{_bindir}/chamfer_volume
%{_bindir}/chop_tags
%{_bindir}/clamp_volume
%{_bindir}/classify_sulcus
%{_bindir}/clean_surface_labels
%{_bindir}/clip_tags
%{_bindir}/close_surface
%{_bindir}/cluster_volume
%{_bindir}/coalesce_lines
%{_bindir}/compare_left_right
%{_bindir}/compare_left_right_groups
%{_bindir}/compare_lengths
%{_bindir}/composite_images
%{_bindir}/composite_minc_images
%{_bindir}/composite_volumes
%{_bindir}/compute_bounding_view
%{_bindir}/compute_resels
%{_bindir}/concat_images
%{_bindir}/contour_slice
%{_bindir}/convex_hull
%{_bindir}/count_thresholded_volume
%{_bindir}/create_2d_sheet
%{_bindir}/create_2d_surface
%{_bindir}/create_box
%{_bindir}/create_four_volumes
%{_bindir}/create_label_map
%{_bindir}/create_landmark_full_volume
%{_bindir}/create_mahalanobis
%{_bindir}/create_surface_interpolation_lsq
%{_bindir}/create_warping_points
%{_bindir}/diff_mahalanobis
%{_bindir}/dilate_volume
%{_bindir}/dilate_volume_completely
%{_bindir}/dim_image
%{_bindir}/dump_deformation_distances
%{_bindir}/dump_points_to_tag_file
%{_bindir}/dump_rms
%{_bindir}/dump_transform
%{_bindir}/dump_uv
%{_bindir}/evaluate
%{_bindir}/extract_largest_line
%{_bindir}/extract_tag_slice
%{_bindir}/fill_sulci
%{_bindir}/find_buried_surface
%{_bindir}/find_image_bounding_box
%{_bindir}/find_peaks
%{_bindir}/find_surface_distances
%{_bindir}/find_tag_outliers
%{_bindir}/find_vertex
%{_bindir}/find_volume_centroid
%{_bindir}/fit_3d
%{_bindir}/fit_curve
%{_bindir}/fit_curve2
%{_bindir}/flatten_polygons
%{_bindir}/flatten_sheet
%{_bindir}/flatten_sheet3
%{_bindir}/flatten_to_sphere
%{_bindir}/flatten_to_sphere2
%{_bindir}/flip_tags
%{_bindir}/flip_volume
%{_bindir}/f_prob
%{_bindir}/gaussian_blur_peaks
%{_bindir}/get_tic
%{_bindir}/group_diff
%{_bindir}/histogram_volume
%{_bindir}/intensity_statistics
%{_bindir}/interpolate_tags
%{_bindir}/labels_to_rgb
%{_bindir}/label_sulci
%{_bindir}/lookup_labels
%{_bindir}/make_diff_volume
%{_bindir}/make_geodesic_volume
%{_bindir}/make_gradient_volume
%{_bindir}/make_grid_lines
%{_bindir}/make_line_links
%{_bindir}/make_slice
%{_bindir}/make_sphere_transform
%{_bindir}/make_surface_bitlist
%{_bindir}/map_colours_to_sphere
%{_bindir}/map_sheets
%{_bindir}/map_surface_to_sheet
%{_bindir}/marching_cubes
%{_bindir}/mask_values
%{_bindir}/mask_volume
%{_bindir}/match_tags
%{_bindir}/mincdefrag
%{_bindir}/mincmask
%{_bindir}/mincskel
%{_bindir}/minc_to_rgb
%{_bindir}/minctotag
%{_bindir}/normalize_pet
%{_bindir}/place_images
%{_bindir}/plane_polygon_intersect
%{_bindir}/preprocess_segmentation
%{_bindir}/print_2d_coords
%{_bindir}/print_all_label_bounding_boxes
%{_bindir}/print_all_labels
%{_bindir}/print_axis_angles
%{_bindir}/print_volume_value
%{_bindir}/print_world_value
%{_bindir}/print_world_values
%{_bindir}/random_warp
%{_bindir}/reparameterize_line
%{_bindir}/rgb_to_minc
%{_bindir}/scale_minc_image
%{_bindir}/scan_lines_to_polygons
%{_bindir}/scan_object_to_volume
%{_bindir}/segment_probabilities
%{_bindir}/spherical_resample
%{_bindir}/stats_tag_file
%{_bindir}/subsample_volume
%{_bindir}/surface_mask
%{_bindir}/surface_mask2
%{_bindir}/tags_to_spheres
%{_bindir}/tagtominc
%{_bindir}/tag_volume
%{_bindir}/threshold_volume
%{_bindir}/transform_objects
%{_bindir}/transform_tags
%{_bindir}/transform_volume
%{_bindir}/trimesh_resample
%{_bindir}/trimesh_set_points
%{_bindir}/trimesh_to_polygons
%{_bindir}/two_surface_resample
%{_bindir}/volume_object_evaluate
%{_bindir}/compute_icbm_vols
%{_bindir}/mritotal_suppress
%{_bindir}/multispectral_stx_registration
%{_bindir}/nlfit_smr
%{_bindir}/regional_thickness
%{_bindir}/remap_to_lobes
%{_bindir}/smooth_mask
%{_bindir}/sphere_resample_obj
%{_bindir}/suppress_fat

%changelog
* Thu Sep 24 2026 Morgan Hough <morgan.hough@gmail.com> - 1.6.80-1.20120308git166303d
- Initial package, from the tip of upstream master. CIVET/MNI tier 1
  (docs/civet-licensing.md); the seventh of the eight permissive components.
  The 132 binaries are listed explicitly rather than globbed: a glob hides a
  program that silently stops being built.