frameMerge

frameMerge is a lightweight Python package for merging crystallographic detector frames within HDF5 files - supporting both parallel (multiprocessing) and sequential execution.

Installation

You can pull from pypi with pip

pip install frameMerge

Or you can clone the repo and install it locally:

git clone https://github.com/ryan-odea/frameMerge.git
cd frameMerge 
pip install .

Usage

You can use frameMerge directly from the command line as:

frameMerge --file-name input.h5 \
           --output-file merged.h5 \
           --n-frames 5000 \
           --n-merged-frames 10 \
           --skip-pattern 1 2 \
           --data-location entry/data \
           --data-name data \
           --parallel

or through the Python API

from frameMerge import Merger

m = Merger(
    file_name="input.h5",
    output_file="merged.h5",
    n_frames=5000,
    n_merged_frames=10,
    skip_pattern=[1, 2],
    data_location="entry/data",
    data_name="data"
)
m.process(parallel=True)

On the cluster

On clusters, you may find the example.sbatch in this repo useful.