# PlanTUS -- heuristic planning of transcranial ultrasound (TUS) transducer
# placements on a SimNIBS charm head model (Lueckel, Vijayakumar & Bergmann,
# Brain Stimulation 18(5), 2025). It scores every skin vertex for distance,
# beam angle, skull thickness and no-go regions, lets the user pick one in a
# PySide6/VTK viewer, and exports the pose for Brainsight, Localite, k-Plan,
# SimNIBS and BabelBrain. BabelBrain's "Run PlanTUS" button runs it.
#
# Layout facts the spec depends on (checked against the pinned commit):
# - No pyproject.toml, setup.py or tags. It is a script tree run as
#   `python PlanTUS_wrapper.py`, which finds code/ and resources/ next to
#   itself (resource_path() = dirname(__file__)) and BabelBrain calls it as
#   <PlanTUS root>/PlanTUS_wrapper.py. So the tree is installed as is to
#   %%{_datadir}/plantus, the root BabelBrain is pointed at, and
#   %%{_bindir}/plantus runs the wrapper.
# - 2.0 dropped Connectome Workbench entirely; it still writes optional
#   scene.scene files that wb_view can open, hence Suggests.
# - ImageTransform_4kPlan.py needs FSL's fslswapdim and ANTsPy (neither in
#   Fedora) and serves only k-Plan, a commercial planner: shipped as
#   documentation, not on PATH. kPlan_results_to_nifti() imports ants lazily
#   for the same reason and is not required.
# - potpourri3d (exact geodesic distances for the no-go margin) is optional
#   upstream with an approximate fallback; it is not packaged yet.

%global commit      f790f4ab3b49e48079c2a82710dcdff1d36d1a21
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%global snapdate    20261006

Name:           plantus
Version:        2.0.0^%{snapdate}git%{shortcommit}
Release:        1%{?dist}
Summary:        Heuristic planning of transcranial ultrasound transducer placements

License:        MIT
URL:            https://github.com/mlueckel/PlanTUS
# main at 2026-10-06 (CHANGELOG: v2.0.0 plus fixes); upstream has no tags.
Source0:        %{url}/archive/%{commit}/PlanTUS-%{shortcommit}.tar.gz
# Accept the 1.x flag names (--skip_wb_view, --do_only_trajectory) as hidden
# aliases. BabelBrain 0.8.x passes --skip_wb_view and stock 2.0 rejects it.
# Submitted upstream by the packager.
Patch0:         plantus-legacy-cli-aliases.patch
# create_SimNIBS_position_matrix built a left-handed frame (det -1), so the
# Brainsight and BabelBrain exports were mirror images of the planned pose.
# Submitted upstream by the packager.
Patch1:         plantus-simnibs-frame-handedness.patch
# The wrapper made a PyQt5 QApplication while the viewer and VTK use PySide6
# when it is installed; the mixture aborts as soon as the viewer opens.
# Submitted upstream by the packager.
Patch2:         plantus-viewer-qt-binding.patch

BuildArch:      noarch
BuildRequires:  python3-devel
# %%check imports the planning code (which imports simnibs at module level),
# the viewer, and runs the wrapper's argument parser.
BuildRequires:  python3-simnibs
BuildRequires:  python3-numpy
BuildRequires:  python3-nibabel
BuildRequires:  python3-scipy
BuildRequires:  python3-pyyaml
BuildRequires:  python3-trimesh
BuildRequires:  python3-vtk
BuildRequires:  python3-pyside6

Requires:       python3-simnibs
Requires:       python3-numpy
Requires:       python3-nibabel
Requires:       python3-nilearn
Requires:       python3-scipy
Requires:       python3-pandas
Requires:       python3-pyyaml
Requires:       python3-h5py
Requires:       python3-trimesh
Requires:       python3-vtk
Requires:       python3-pyside6
# charm, which makes the head model PlanTUS starts from, is in python3-simnibs.
# Optional Workbench scenes of the metric maps and placements.
Suggests:       connectome-workbench

%description
PlanTUS helps users of transcranial ultrasonic stimulation (TUS) choose the
most promising transducer placement for sonicating a target region in an
individual head. From a SimNIBS charm head model, the T1 image and a target
mask, it computes per-vertex skin maps of target distance, beam angle,
skin-skull angle, skull thickness and intersections, excludes regions near
the eyes, ears and air cavities, and combines them into a composite score.
The user picks a placement in an interactive PySide6/VTK viewer (or by vertex
number, headless), and PlanTUS writes the transducer pose and an estimated
focus for neuronavigation (Brainsight, Localite) and acoustic simulation
(BabelBrain, k-Plan, SimNIBS).

PlanTUS informs acoustic simulations but does not replace them; placements
should be validated with a full simulation.

%prep
%autosetup -n PlanTUS-%{commit} -p1
rm -rf code/__pycache__
# The tree is run by %%{_bindir}/plantus through python3; nothing in it is
# executed directly, so no file keeps an executable bit or a shebang.
find . -name '*.py' -exec chmod 0644 {} +
sed -i '1{/^#!/d}' PlanTUS_wrapper.py code/*.py

%build
# Nothing to build.

%install
mkdir -p %{buildroot}%{_datadir}/%{name}
cp -pr PlanTUS_wrapper.py code resources %{buildroot}%{_datadir}/%{name}/
# Transducer configuration templates, read with --config / the YAML argument.
cp -p PlanTUS_config_*.yaml %{buildroot}%{_datadir}/%{name}/
%py_byte_compile %{python3} %{buildroot}%{_datadir}/%{name}

mkdir -p %{buildroot}%{_bindir}
cat > %{buildroot}%{_bindir}/%{name} <<EOF
#!/usr/bin/bash
exec %{python3} %{_datadir}/%{name}/PlanTUS_wrapper.py "\$@"
EOF
chmod 0755 %{buildroot}%{_bindir}/%{name}

%check
export QT_QPA_PLATFORM=offscreen
export HOME=$PWD/home; mkdir -p "$HOME"
root=%{buildroot}%{_datadir}/%{name}

# The wrapper's parser: the 2.0 flags are documented, the 1.x aliases parse
# but stay out of --help.
%{python3} "$root/PlanTUS_wrapper.py" --help > help.txt
grep -q -- '--skip_viewer' help.txt
grep -q -- '--placement_only' help.txt
! grep -q -- '--skip_wb_view' help.txt
! grep -q -- '--do_only_trajectory' help.txt

# The planning code and the viewer import from the installed tree, and the
# exported pose frames are right-handed (Patch1).
PYTHONPATH="$root/code" %{python3} - <<'EOF'
import numpy as np
import PlanTUS
import Viewer  # PySide6 + VTK's Qt interactor, offscreen
rng = np.random.default_rng(1)
for _ in range(50):
    z = rng.normal(size=3)
    for roll in (0.0, 37.0, -90.0):
        M = PlanTUS.create_SimNIBS_position_matrix([10.0, -20.0, 30.0], z, roll)
        d = np.linalg.det(M[:3, :3])
        assert abs(d - 1.0) < 1e-9, (z, roll, d)
        assert np.allclose(M[:3, 2], z / np.linalg.norm(z))
print("PlanTUS and Viewer import; SimNIBS pose frames right-handed")
EOF

# The wrapper picks the viewer's Qt binding (Patch2).
grep -q 'from PySide6.QtWidgets import QApplication, QDialog, QVBoxLayout' "$root/PlanTUS_wrapper.py"

%files
%license LICENSE.md
%doc README.md CHANGELOG.md ImageTransform_4kPlan.py
%{_bindir}/%{name}
%{_datadir}/%{name}/

%changelog
* Tue Oct 13 2026 Morgan Hough <morgan.hough@gmail.com> - 2.0.0^20261006gitf790f4a-1
- Initial package. Carries three fixes submitted upstream: the 1.x flag names
  as hidden aliases (so BabelBrain 0.8.x can call it), right-handed SimNIBS,
  Brainsight and BabelBrain pose exports, and one Qt binding for the viewer.