# See docs/fluorender-plan.md for the survey behind this spec: why a master
# snapshot and not the v2.34.1 tag, the bundled-code inventory, the licence
# audit and the upstream asks.
#
# master df5d443 (2026-08-05) is 40 commits past v2.34.1 (2026-05-20). The
# snapshot is what has the Linux install layout this package relies on:
# GetDataRoot() looks in /usr/share/fluorender (Utility/Directory.h), user
# state goes to $XDG_CONFIG_HOME/FluoRender, and the readlink() buffer that the
# tag left unterminated is fixed. It also builds against OpenCV 5, which the
# COPR buildroot carries. Master itself did not compile on Linux (patch 1).
%global commit      df5d443cc16afaada83aacebcb42882f65bb4aeb
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%global snapdate    20260805

Name:           fluorender
Version:        2.34.1^%{snapdate}git%{shortcommit}
# Explicit, not %%autorelease (ci/PROCEDURES.md golden rule 3).
Release:        0.1%{?dist}
Summary:        Interactive rendering and analysis of fluorescence microscopy volumes

# FluoRender: MIT (LICENSE.txt; per-file headers, (c) 2026 SCI Institute).
# Compiled in and bundled (see the Provides below):
#   File/confini.{c,h}        libconfini 1.16.4    GPL-3.0-or-later
#   File/pole.{cpp,h}         POLE                 BSD-2-Clause
#   File/tiny-json.{c,h}      tiny-json            MIT
#   Glad/                     glad 2.0.8 output    (WTFPL OR CC0-1.0) AND Apache-2.0
#   Glad/include/KHR/khrplatform.h                 MIT-Khronos-old
#   Graphics/glm.{cpp,h}      Nate Robins' Wavefront OBJ reader (glm.c, 1997,
#                             2000). The file states no licence. It was
#                             distributed with Mark Kilgard's GLUT 3.7 (the
#                             "smooth" demo) and is still carried by Mesa as
#                             mesa/demos src/objviewer/glm.c, which Fedora
#                             ships in mesa-demos under License: MIT. Kept on
#                             that precedent, with no extra License term;
#                             confirming its terms is an open upstream ask
#                             before any Fedora package review (see the plan).
# Shipped as data: Templates/d3.v4.min.js, d3 4.13.0, BSD-3-Clause.
# Because libconfini is compiled into the one executable, the binary as a
# whole is distributable only under GPL-3.0-or-later terms.
# Removed by fluorender-clean.sh (not in the SRPM): the Nikon ND2 SDK binaries,
# Microsoft Holographic Remoting DLLs, nuget.exe, VC_redist.x64.exe, the
# Java_Code jars (including SlideBook6Reader.jar and bio-formats), and the
# Looking Glass Bridge SDK headers (FluoRender/BridgeRuntime, no licence
# statement; Looking Glass support is compiled out, see Patch5).
# Deleted in %%prep (in the SRPM, not in the binary RPM): Wacom WinTab sample
# code (Windows only), tinyxml2 10.0.0 (system copy used), the FreeFont .ttf
# files (system fonts used), upstream's modified wxWidgets aui sources.
License:        MIT AND GPL-3.0-or-later AND BSD-2-Clause AND BSD-3-Clause AND Apache-2.0 AND (WTFPL OR CC0-1.0) AND MIT-Khronos-old
URL:            https://github.com/SCIInstitute/fluorender

# NOT an upstream tarball: fluorender-clean.sh removes prebuilt binaries that
# Fedora cannot ship (see the script's header). Same arrangement as invesalius
# and opencv in this repo: the cleaned tarball goes in this project's COPR
# dist-git lookaside, content-addressed by md5, so the package builds from git.
# Upstream URL of the uncleaned tree, for reference:
#   %%{url}/archive/%%{commit}/fluorender-%%{commit}.tar.gz
%global copr_lookaside https://copr-dist-git.fedorainfracloud.org/repo/pkgs/mhough/neurofedora/%{name}
%global cleanmd5       385908b575fd2f407346ffa3b9ad8e31
Source0:        %{copr_lookaside}/%{name}-clean-%{shortcommit}.tar.xz/md5/%{cleanmd5}/%{name}-clean-%{shortcommit}.tar.xz
Source1:        fluorender-clean.sh
Source2:        fluorender-wrapper.sh
Source3:        fluorender.desktop
Source4:        fluorender.metainfo.xml

# Use system libraries only: shared system wxWidgets, openvr, OpenXR, OpenJPEG
# link fix, tinyxml2; Java_Code copy only if present. Adds the CMake option
# FLUORENDER_USE_SYSTEM_LIBS (default OFF).
Patch0:         fluorender-system-libraries.patch
# master does not compile on Linux: debugging output added 2026-07-13 uses the
# Windows BOOL type. Use GLboolean.
Patch1:         fluorender-glboolean.patch
# Fedora has wxWidgets 3.2.9; upstream now targets 3.3. Every change is behind
# wxCHECK_VERSION(3, 3, 0): wxAuiSerializer (tab layouts are not saved on 3.2),
# wxApp::SetAppearance, wxDisplay::GetFromRect, wxAUI_NB_MULTILINE, range-for
# over wxGridCellCoordsArray, and one call that only exists in upstream's own
# modified wxAuiNotebook.
Patch2:         fluorender-wx32.patch
# wxGLContextAttrs::PlatformDefaults() is what sets x11Direct on GLX; without
# it glXCreateContext gets an uninitialised Bool and the X server answers
# BadValue, so FluoRender exited before showing a window under Xvfb.
Patch3:         fluorender-glx-context-defaults.patch
# OnInit() chdirs to the executable's directory before the command line is
# parsed, so relative file and -m movie paths resolved under /usr/libexec.
Patch4:         fluorender-relative-cmdline-paths.patch
# Looking Glass holographic displays need the Bridge SDK headers, which carry
# no licence statement (removed from the tarball by fluorender-clean.sh), and
# the proprietary Looking Glass Bridge runtime, which Fedora cannot ship. Adds
# the CMake option FLUORENDER_LOOKINGGLASS (OFF under FLUORENDER_USE_SYSTEM_LIBS)
# and guards every Looking Glass code path, the light-field shader, the
# "Holography" toolbar button and the Settings controls. Stereo/VR (OpenXR,
# openvr) is unaffected.
Patch5:         fluorender-no-lookingglass.patch

# OpenCL kernels, dlib, OpenCV 5 and hdf5 have only been tried on x86_64;
# nothing here is x86-specific, but aarch64 has not been built.
BuildRequires:  cmake
BuildRequires:  gcc
BuildRequires:  gcc-c++
BuildRequires:  make
BuildRequires:  wxGTK-devel >= 3.2
BuildRequires:  libglvnd-devel
BuildRequires:  zlib-devel
BuildRequires:  libtiff-devel
BuildRequires:  libpng-devel
BuildRequires:  libjpeg-turbo-devel
BuildRequires:  boost-devel
BuildRequires:  bzip2-devel
BuildRequires:  dlib-devel
BuildRequires:  eigen3-devel
BuildRequires:  opencv-devel
BuildRequires:  python3-devel
BuildRequires:  hdf5-devel
# Only for <jni.h>: the JVM is dlopen()ed at run time from a user-set path.
BuildRequires:  java-devel
BuildRequires:  pkgconfig(libavcodec)
BuildRequires:  pkgconfig(libavformat)
BuildRequires:  pkgconfig(libavutil)
BuildRequires:  pkgconfig(libswscale)
BuildRequires:  pkgconfig(libswresample)
BuildRequires:  freetype-devel
BuildRequires:  glm-devel
BuildRequires:  ocl-icd-devel
BuildRequires:  opencl-headers
BuildRequires:  openjpeg2-devel
BuildRequires:  openxr-devel
BuildRequires:  openvr-devel
BuildRequires:  teem-devel
BuildRequires:  tinyxml2-devel
# dlib's exported CMake link interface names these libraries but dlib-devel
# does not require their -devel packages; without them the final link fails
# with "No rule to make target /usr/lib64/libflexiblas.so" and -ljxl.
BuildRequires:  flexiblas-devel
BuildRequires:  sqlite-devel
BuildRequires:  pkgconfig(libavdevice)
BuildRequires:  pkgconfig(libavfilter)
BuildRequires:  libjxl-devel
# %%check: render a volume under Xvfb with Mesa llvmpipe.
BuildRequires:  xorg-x11-server-Xvfb
BuildRequires:  mesa-dri-drivers
BuildRequires:  python3-pillow
BuildRequires:  desktop-file-utils
BuildRequires:  /usr/bin/appstream-util

# Fonts/ ships GNU FreeFont; the package links the system copies instead.
Requires:       gnu-free-sans-fonts
Requires:       gnu-free-mono-fonts
Requires:       gnu-free-serif-fonts
Requires:       hicolor-icon-theme
Recommends:     %{name}-data = %{version}-%{release}

Provides:       bundled(libconfini) = 1.16.4
Provides:       bundled(pole)
Provides:       bundled(tiny-json)
Provides:       bundled(glad2) = 2.0.8
Provides:       bundled(js-d3) = 4.13.0

%description
FluoRender is an interactive tool for multichannel fluorescence microscopy
from the SCI Institute (University of Utah). It renders confocal and
light-sheet volume stacks in real time, with per-channel transfer functions,
clipping planes and colocalization, and supports painting-based selection,
connected-component analysis and tracking over time, rulers and
measurements, OpenCL image filters and movie export.

It reads TIFF stacks, NRRD, Olympus OIB/OIF, Zeiss LSM and CZI, Leica
LIF/LOF, DICOM and PrairieView XML. Not in this build: Nikon ND2 files
(the ND2 SDK is proprietary), Looking Glass holographic displays (the
Looking Glass Bridge is proprietary) and the ImageJ/Bio-Formats bridge.

%package data
Summary:        Sample volumes for FluoRender
License:        MIT
BuildArch:      noarch
Requires:       %{name} = %{version}-%{release}

%description data
Sample data shipped with FluoRender: a three-channel zebrafish brain (used
by upstream's benchmark) and small density and distance fields.

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

# Windows-only code, with system replacements, or not built on Linux.
rm -r FluoRender/FluoRender/WacomUtils FluoRender/FluoRender/XInput
rm FluoRender/Glad/src/wgl.c FluoRender/Glad/include/glad/wgl.h
rm FluoRender/FluoRender/File/tinyxml2.cpp FluoRender/FluoRender/File/tinyxml2.h
# Upstream's modified copies of wxWidgets' aui sources, for its static wx build.
rm -r wxWidgets
rm Fonts/*.ttf

%build
%cmake \
  -DFLUORENDER_USE_SYSTEM_LIBS:BOOL=ON \
  -DFLUORENDER_LOOKINGGLASS:BOOL=OFF \
  -DJAVA_HOME:PATH=%{_jvmdir}/java
%cmake_build

%install
# Upstream has no install rules; the build tree's bin/ is the portable layout.
B=%{_vpath_builddir}/bin
install -Dpm 0755 $B/FluoRender %{buildroot}%{_libexecdir}/%{name}/FluoRender
install -Dpm 0755 %{SOURCE2} %{buildroot}%{_bindir}/%{name}
sed -i 's|/usr/libexec|%{_libexecdir}|' %{buildroot}%{_bindir}/%{name}

# GetDataRoot() finds /usr/share/fluorender by its Scripts/ directory.
# Main.cpp's InitializeUserSettings() copies CL_code, Commands, Database,
# Scripts, Templates and the two .xml files to ~/.config/FluoRender once per
# major.minor version; Fonts and Data are read in place.
install -d %{buildroot}%{_datadir}/%{name}
for d in CL_code Commands Database Scripts Templates Data; do
  cp -pr $B/$d %{buildroot}%{_datadir}/%{name}/
done
install -pm 0644 $B/fluorender.xml $B/fluorender_default.xml %{buildroot}%{_datadir}/%{name}/
install -d %{buildroot}%{_datadir}/%{name}/Fonts
for f in FreeMono FreeMonoBold FreeMonoBoldOblique FreeMonoOblique \
         FreeSans FreeSansBold FreeSansBoldOblique FreeSansOblique \
         FreeSerif FreeSerifBold FreeSerifBoldItalic FreeSerifItalic; do
  ln -s ../../fonts/gnu-free/$f.ttf %{buildroot}%{_datadir}/%{name}/Fonts/$f.ttf
done

for s in 48 128; do
  install -Dpm 0644 Install/Ubuntu/fluorender/assets/icons/hicolor/${s}x${s}/apps/fluorender.png \
    %{buildroot}%{_datadir}/icons/hicolor/${s}x${s}/apps/%{name}.png
done
desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE3}
install -Dpm 0644 %{SOURCE4} %{buildroot}%{_metainfodir}/%{name}.metainfo.xml

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

# Upstream has no test suite (Tester/ is Windows-only). Render a synthetic
# volume headless instead: a 64x64x32 uint8 NRRD with a bright sphere centred
# at x=40, y=28 on a dim z gradient, loaded through teem, rendered by the GL
# volume renderer on llvmpipe, and written out by the command-line movie
# export (-m). The first frame must show a red sphere right of the volume's
# centre, and nothing in green or blue.
mkdir -p check/home check/mov
export HOME=$PWD/check/home XDG_CONFIG_HOME=$PWD/check/home/.config
python3 - check/sphere.nrrd <<'EOF'
import sys
nx, ny, nz = 64, 64, 32
vox = bytearray()
for z in range(nz):
    for y in range(ny):
        for x in range(nx):
            r2 = (x - 40) ** 2 + (y - 28) ** 2 + ((z - 16) * 2.0) ** 2
            vox.append(min(255, (220 if r2 < 18 * 18 else 0) + 2 * z))
with open(sys.argv[1], "wb") as f:
    f.write(b"NRRD0004\ntype: uint8\ndimension: 3\nsizes: 64 64 32\n"
            b"spacings: 1 1 2\nencoding: raw\n\n")
    f.write(bytes(vox))
EOF
exec 5>check/xdisplay
Xvfb -displayfd 5 -screen 0 1280x800x24 -nolisten tcp > check/xvfb.log 2>&1 &
xvfb=$!
for i in $(seq 50); do [ -s check/xdisplay ] && break; sleep 0.2; done
export DISPLAY=:$(cat check/xdisplay)
export LIBGL_ALWAYS_SOFTWARE=1 GDK_BACKEND=x11 NO_AT_BRIDGE=1
%{_vpath_builddir}/bin/FluoRender check/sphere.nrrd -m check/mov/f.tif > check/run.log 2>&1 &
app=$!
# Frame 000 is complete once frame 001 exists. Allow 4 minutes on a slow builder.
for i in $(seq 240); do
  ls check/mov/f_*1.tif >/dev/null 2>&1 && break
  kill -0 $app 2>/dev/null || break
  sleep 1
done
kill $app 2>/dev/null || :
kill $xvfb 2>/dev/null || :
wait $app 2>/dev/null || :
cat check/run.log | grep -v -e '^$' -e 'Gtk-CRITICAL' -e 'for_size smaller' | tail -n 20 || :
python3 - <<'EOF'
import glob
from PIL import Image
frames = sorted(glob.glob("check/mov/f_*.tif"))
assert frames, "no movie frame was written"
im = Image.open(frames[0]).convert("RGB")
w, h = im.size
px = im.load()
red = [(x, y) for y in range(h) for x in range(w) if px[x, y][0] > 200]
box = [(x, y) for y in range(h) for x in range(w) if px[x, y][0] > 0]
gb = max(max(px[x, y][1], px[x, y][2]) for y in range(0, h, 4) for x in range(0, w, 4))
assert len(red) > 0.02 * w * h, f"sphere missing: {len(red)} bright pixels of {w*h}"
assert gb < 16, f"unexpected green/blue signal {gb}"
x0 = min(p[0] for p in box); x1 = max(p[0] for p in box)
cx = sum(p[0] for p in red) / len(red)
fx = (cx - x0) / (x1 - x0)
print(f"{frames[0]}: {w}x{h}, {len(red)} sphere pixels, centroid at {fx:.3f} of the volume width")
assert 0.55 < fx < 0.70, f"sphere centroid {fx:.3f}, expected ~0.625"
EOF

%files
%license LICENSE.txt
%doc README.md
%{_bindir}/%{name}
%{_libexecdir}/%{name}/
%dir %{_datadir}/%{name}
%{_datadir}/%{name}/CL_code/
%{_datadir}/%{name}/Commands/
%{_datadir}/%{name}/Database/
%{_datadir}/%{name}/Fonts/
%{_datadir}/%{name}/Scripts/
%{_datadir}/%{name}/Templates/
%{_datadir}/%{name}/fluorender.xml
%{_datadir}/%{name}/fluorender_default.xml
%{_datadir}/applications/%{name}.desktop
%{_datadir}/icons/hicolor/*/apps/%{name}.png
%{_metainfodir}/%{name}.metainfo.xml

%files data
%{_datadir}/%{name}/Data/

%changelog
* Sat Oct 10 2026 Morgan Hough <morgan.hough@gmail.com> - 2.34.1^20260805gitdf5d443-1
- Initial package: master snapshot df5d443 (40 commits after v2.34.1), from a
  tarball cleaned of the proprietary Nikon ND2 SDK, Microsoft DLLs, Windows
  installers, prebuilt Java jars and the unlicensed Looking Glass Bridge SDK
  headers; Looking Glass support is compiled out. Built against Fedora's
  shared wxGTK 3.2, system tiff/png/jpeg/zlib/boost/dlib/OpenCV/hdf5/ffmpeg/
  freetype/glm/teem/OpenJPEG/OpenXR/openvr/tinyxml2 and GNU FreeFont. Fixes for the Linux build
  (BOOL), wx 3.2, an uninitialised GLX context flag and relative command-line
  paths. Wrapper runs it through XWayland. %%check renders a volume headless.