Erik Fröjdh
d1e432f8ca
Second part of splitting up dev/gap. Only the in-memory transform; no reader changes. - `GapPixels` and `ModuleGaps` configure 2 pixel gaps at the chip boundaries inside each Jungfrau or Eiger module and, only when module gaps are set, gaps between modules. Gap pixels get a fill value or, with `split_counts`, half of the neighbouring double size pixel. - `insert_gap_pixels` and `gapped_shape` apply the transform to an image in memory. Gap positions follow detector coordinates, so a ROI receives exactly the gaps that fall inside it. - Python bindings, tests and docs for the above. Chip and module sizes are fixed at 256 and 1024x512, so there is no detector type or quad argument: an Eiger quad is 512x512 and its only chip boundaries are at pixel 256. Reading raw files with gaps comes in the next PR.
aare
Data analysis library for PSI hybrid detectors
Documentation
Detailed documentation including installation can be found in Documentation
License
This project is licensed under the MPL-2.0 license. See the LICENSE file or https://www.mozilla.org/en-US/MPL/ for details.
Two files contain code from other projects and keep their original licenses:
include/aare/ProducerConsumerQueue.hppis Apache-2.0, from folly by Meta Platforms.src/NumpyHelpers.cppis MIT, from libnpy by Leon Merten Lohse.
The full license texts are in the LICENSES directory.
The Python wheels and conda packages also contain Minuit2
(LGPL-2.1-or-later), {fmt} and nlohmann/json (MIT), and pybind11
(BSD-3-Clause), which CMake downloads at build time. See
THIRD-PARTY-NOTICES.txt for their notices.
Build and install
Prerequisites
- cmake >= 3.14
- C++17 compiler (gcc >= 8)
- python >= 3.10
Development install (for Python)
git clone git@github.com:slsdetectorgroup/aare.git --branch=v1 #or using http...
mkdir build
cd build
#configure using cmake
cmake ../aare -DAARE_PYTHON_BINDINGS=ON
#build (replace 4 with the number of threads you want to use)
make -j4
Now you can use the Python module from your build directory
import aare
f = aare.File('Some/File/I/Want_to_open_master_0.json')
To run from other folders either add the path to your conda environment using conda-build or add the module to your PYTHONPATH
export PYTHONPATH=path_to_aare/aare/build:$PYTHONPATH
Install using conda/mamba
#enable your env first!
conda install aare -c slsdetectorgroup # installs latest version
Install to a custom location and use in your project
Working example in: https://github.com/slsdetectorgroup/aare-examples
#build and install aare
git clone git@github.com:slsdetectorgroup/aare.git --branch=v1 #or using http...
mkdir build
cd build
#configure using cmake
cmake ../aare -DCMAKE_INSTALL_PREFIX=/where/to/put/aare
#build (replace 4 with the number of threads you want to use)
make -j4
#install
make install
#Now configure your project
cmake .. -DCMAKE_PREFIX_PATH=SOME_PATH
Local build of conda pkgs
conda build . --variants="{python: [3.11, 3.12, 3.13]}"
Developer's guide
We are looking forward to your contributions via pull requests!
If you want to fix an existing bug or propose a new feature:
- Install
pre-commitpython package and setup itpre-commit install - Create a new branch with
git branch branch_name - Implement your changes and make a commit (
pre-commitwill check your code automatically) - Push your commit and open a pull request if needed