acquire-imaging 0.1.4

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acquire-imaging

This python package provides a multi-camera video streaming library focusing on performant microscopy.

Note This is an early stage project. If you find it interesting please reach out!

Support for:

• Up to two independent video streams
• Camera support:
  • Hamamatsu Orca Fusion BT (C15440-20UP) (windows only)
  • Vieworks VC-151MX-M6H00
• Streaming file format support:
  • Tiff
  • Zarr v2

Installation

python -m pip install acquire-imaging

Usage

See the tests for more examples.

The provided napari plugin is a good example of how to stream for visualization.

List devices

import acquire
print(acquire.Runtime().device_manager().devices())

Finite triggered acquisition

import acquire
runtime=acquire.Runtime()
dm=runtime.device_manager()

props=runtime.get_configuration()
# select the first Hamamatsu camera
props.video[0].camera.identifier = dm.select(DeviceKind.Camera, "hamamatsu.*")
# stream to zarr
props.video[0].storage.identifier = dm.select(DeviceKind.Storage, "zarr")
props.video[0].storage.settings.filename="out.zarr"
props.video[0].camera.settings.shape = (2304, 2304)
props.video[0].camera.settings.pixel_type = SampleType.U16
props.video[0].max_frame_count = 100
props=runtime.configure(props)

runtime.start()
runtime.stop() # wait for acquisition to complete

Development

We welcome contributors. The following will help you get started building the code.

Environment

Requires

• CMake 3.23+ (download page or via chocolatey)
• A C++20 compiler (Microsoft Visual Studio Community download page, or clang)
• Rust (via rustup, see install page)
• conda (optional; via miniconda)
• libclang >= v5.0 (on windows via choco choco install llvm or, on osx, via brew brew install llvm)

It's strongly recommended you create a python environment for development

conda create --name acquire python=3.11
conda activate acquire

Build

conda activate acquire
git submodule update --init --recursive
pip install maturin
maturin build -i python

Important When updating the 'acquire-video-runtime' (the c api), to need to manually trigger a rebuild by touching wrapper.h.

git submodule update # updates acquire-video-runtime
touch wrapper.h # will trigger a rebuild
python -m build

This package depends on a submodule (acquire-video-runtime) and binaries from the following Acquire drivers:

• acquire-driver-common
• acquire-driver-hdcam
• acquire-driver-egrabber
• acquire-driver-zarr

The build script will automatically try to fetch the binaries from GitHub releases. In order to configure which release of each driver to use, you can set the value in drivers.json:

{
  "acquire-driver-common": "0.1.0",
  "acquire-driver-hdcam": "0.1.0",
  "acquire-driver-egrabber": "0.1.0",
  "acquire-driver-zarr": "0.1.0"
}

These values can be set to a specific version, or to nightly for nightly builds.

Develop

pip install -e ".[testing]"
pytest -s --tb-short --log-cli-level=0

This project uses pre-commit to run required checks as git hooks.

pip install pre-commit
pre-commit install

Troubleshooting

Maturin can't find a python interpreter

Maturin is a command line tool associated with pyo3. It helps automate the build and packaging process. It's invoked by setuptools during a build.

1. Double-check you've activated the right conda environment.
2. Try maturin build -i python

This seems to happen on windows in anaconda environments when multiple python interpreters are available on the path.

It seems to happen less frequently when invoked via pip - pip install -e . will end up invoking maturin.

Working with an editable install, how do I update the build?

It depends on what you changed:

• acquire-video-runtime (c/c++ code): touch wrapper.h; maturin develop
• rust code: maturin develop