paullo9 / emdfile

interfaces with EMD 1.0 files

emdfile

EMD (Electron Microscopy Dataset) 1.0 is an HDF5 based file format which is designed to carry arbitrary data and metadata. An overview of the file specification can be found here.

emdfile is a Python package defining write and read functions and a set of classes which together interface between EMD 1.0 files and Python runtime objects. The classes are designed to quickly build, save to, and read from filetree-like representations of data and metadata, and is built on HDF5+h5py.

Installation

Run

pip install emdfile

Or, to install from source code, you can clone this repository and from the distribution level directory (i.e. where pyproject.toml lives) run

pip install .

Examples and syntax

For a few simple examples... ((this is coming extremely soon ish!))

For a longer, narrative intro example, see tutorials/emd_intro_example.ipynb.

For a detailed walkthrough of the syntax, see tutorials/emd_package_walkthrough.ipynb.

emdfile is designed to support I/O in downstream Python modules and packages. When tutorials/test_custom_classes.py is run as a script, it makes, saves, loads, then prints the contents of the data carrying classes defined in the tutorials/sample_custom_emd_classes Python module.