samcore
Python package and C++ library for Scanning Acoustic Microscopy (SAM) core data processing.
Cloning
The repository uses a git submodule for the bundled FFT backend
(external/pocketfft, a header-only dependency). Clone with submodules:
git clone --recurse-submodules git@github.com:FreiburgBDS/samcore.git
If you already cloned without them (or want to update them):
git submodule update --init --recursive
Installation & Dependencies
Install the system dependencies for your platform (below), then either
pip install . for the Python package or build the C++ library with CMake.
Dependencies
Requires a C++20 compiler and CMake. Dependencies:
- HDF5 (C++ bindings): used for
.h5sam/.h5samdfile I/O. Obtained via the nix dev shell, a distro package, orHDF5_ROOT. - PocketFFT: FFT backend, vendored as a git submodule
(
external/pocketfft). - nanobind + numpy: build-time dependencies of the Python package (installed automatically by pip).
Nix:
nix-shell
Arch Linux
sudo pacman -S --needed --noconfirm base-devel cmake ninja hdf5 python-pip
Debian / Ubuntu
sudo apt-get update && sudo apt-get -y install cmake ninja-build build-essential \
libhdf5-dev pkg-config python3-dev python3-pip
Fedora
sudo dnf install -y cmake ninja-build gcc-c++ hdf5-devel python3-devel python3-pip
Windows / macOS
Both platforms are built with LLVM Clang and Ninja via conda-forge: AppleClang on macOS ships no OpenMP, and MSVC only implements the outdated OpenMP 2.0.
conda install -c conda-forge clangxx llvm-openmp hdf5 cmake ninja
On macOS, also point the build at the active conda prefix so CMake finds
HDF5/OpenMP and the compiler finds omp.h:
export CC="$CONDA_PREFIX/bin/clang"
export CXX="$CONDA_PREFIX/bin/clang++"
export HDF5_ROOT="$CONDA_PREFIX"
export CMAKE_PREFIX_PATH="$CONDA_PREFIX"
export CPATH="$CONDA_PREFIX/include"
export LIBRARY_PATH="$CONDA_PREFIX/lib"
Python package (samcore)
Installation
pip install .
If you followed the recommended Conda setup on Windows or macOS, point CMake at the Clang toolchain:
Windows (PowerShell):
pip install . -C cmake.args="-G Ninja" -C cmake.args="-DCMAKE_CXX_COMPILER=clang++" -C cmake.args="-DCMAKE_C_COMPILER=clang"
macOS (with the environment variables from above exported):
pip install . -C cmake.args="-G Ninja"
Usage
from samcore import SAMScan, SAMDataset
scan = SAMScan("testdata.h5sam") # .h5sam files
img = scan.image_absmax() # (nlines, cols)
dataset = SAMDataset([scan])
dataset.preprocess("lp", cutoff=10.0, fs=2.5e3)
scan.data and dataset.X are zero-copy numpy views of the C++ buffers;
SAMScan(path, mmap=True) keeps h5sam signal data on disk
until first accessed.
The wheel ships .pyi type stubs plus a py.typed marker (generated at
build time by nanobind's stubgen), so static type checkers and IDEs see the
full typed API.
C++ library (libsamcore)
Build
cmake -B build -G Ninja
cmake --build build
On Windows or macOS, set up the conda toolchain from above first (including the exported variables on macOS) so CMake finds Clang and HDF5.
Optional executables (bench, gen_data, see below):
cmake -B build -G Ninja -DSAMCORE_BUILD_EXECUTABLES=ON
cmake --build build
Usage
#include <samcore/sam_scan.hpp>
#include <samcore/sam_dataset.hpp>
int main() {
auto scan = samcore::sam_scan::from_file("testdata.h5sam"); // .h5sam files
auto img = scan.image_absmax();
samcore::sam_dataset dataset({scan});
samcore::preprocess_args args;
args.cutoff = 10.0;
args.fs = 2.5e3;
dataset.preprocess("lp", args);
}
Install with cmake --install build and consume in downstream CMake projects using
find_package(samcore REQUIRED) and linking samcore::samcore.
Note: OpenMP is an implementation detail of the static library and is not
propagated through the CMake package. Consumers linking libsamcore.a
enable it themselves (find_package(OpenMP) + link OpenMP::OpenMP_CXX).
Developers
Generate Stubs
The wheel ships .pyi type stubs plus a py.typed marker. They are
generated automatically at build time by nanobind's stubgen: a CMake custom
command in the SAMCORE_BUILD_PYTHON block stages an importable copy of the
package (pure-Python modules + generated _version.py + the compiled
extension) and runs python -m nanobind.stubgen. No manual step is needed
when running pip install ..
To regenerate manually after installing nanobind into your environment:
python -m nanobind.stubgen -m samcore -m samcore._samcore -m samcore._scan \
-m samcore._labels -m samcore._dataset -m samcore._io -M py.typed
Executables
Optional tools, built with -DSAMCORE_BUILD_EXECUTABLES=ON:
bench- OpenMP scaling smoke benchmark (./bench [scans_x scans_y scanlen]).gen_data- deterministic random test-data generator (gated sine burst + gaussian noise, int8), writing.h5sam(with per-scan starts) or a multi-cube.h5samd. Used to (re)generatetests/data/testdata.h5samandtests/data/testdata.h5samd.
Tests
# C++ (googletest) - debug build with sanitizers
cmake -B build-debug -G Ninja -DCMAKE_BUILD_TYPE=Debug
cmake --build build-debug
ASAN_OPTIONS=detect_leaks=1:halt_on_error=1 \
UBSAN_OPTIONS=halt_on_error=1 \
ctest --test-dir build-debug --output-on-failure
# Python (pytest)
pip install .
pytest tests/python
Test data ships in tests/data/ (override with SAMCORE_TEST_DATA_DIR).
Release builds use -O2 -ffast-math -flto; Debug enables ASan+UBSan+LSan.
1 maintainer
Release files for samcore 0.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| samcore-0.1.0.tar.gz | 7.1 MB | Details |
Built distributions (wheels)
Total release size: 378.7 MB
Release files / samcore-0.1.0.tar.gz
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| Download URL | samcore-0.1.0-cp39-cp39-macosx_11_0_arm64.whl |
|---|---|
| Size | 21.4 MB |
| Tags | CPython 3.9 macOS 11.0+ ARM64 |
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SHA-256 checksum How to use checksums |
f94918435178291827722a31222cbc204366cf31677aa40d28233c6c5952bf94
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BLAKE2b-256 checksum How to use checksums |
01399597e69adc9ee1e9d4767a429f216ba48b2b35a0758b011cd9790205ff2e
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
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Signed by GitHub Actions, verified by PyPI on Sep 21, 2026.
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