A script to create Photon-HDF5 files.
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README.md

phforge

What is it?

phforge is a script to create Photon-HDF5 files starting from two files:

  • a YAML file containing the metadata
  • a (temporary) HDF5 file containing only the photon_data arrays

The main purpose of this script is enabling programs (e.g. acquisition software) in any programming languages to create valid Photon-HDF5 files with minimal effort. Under the hood, phforge uses the phconvert library to assure compliance with the Photon-HDF5 specs and to simplify creating the file.

How to use?

A program wanting to create a Photon-HDF5 file, needs to first create a temporary HDF5 file (with photon timestamps) and a text YAML file with the metadata. With these two input files, phforge can save a Photon-HDF5 file.

The temporary HDF5 file needs to contain the photon-data arrays (timestamps, detectors, nanotimes). The metadata file contains all the Photon-HDF5 fields except for the photon-data arrays. Examples of both YAML and HDF5 files can be found in the example_data folder.

Finally, to create a Photon-HDF5 file run phforge as follows:

phforge metadata_file hdf5_file out_file

The script creates an in-memory Photon-HDF5 representation (based on nested dictionaries) joining the metadata structure from the YAML file and the numeric arrays from the temporary HDF5 file. Then, it uses phconvert's save_photon_hdf5() function to save a new Photon-HDF5 file.

Call phforge -h to print usage information.

How to install phforge?

It is recommended to first instal a conda distribution (either Anaconda or Miniconda3). The installation adds the phforge script to the system path so that it can be directly called from any shell.

Installation from source (provisional)

You can install phforge from source as described here.

First install phconvert and h5py with:

conda install phconvert h5py -c conda-forge

Then download and extract phforge archive from GitHub, open the terminal, cd into phforge source folder and type:

pip install .

Installation from conda packages (not yet available)

Soon, it will be possible to install phforge and all the dependencies (including phconvert) with a single command:

conda install phforge -c conda-forge  # not yet available

Dependencies

  • python 3.4 (or later, recommended) or 2.7 (legacy)
  • pyyaml (tested on 3.11)
  • h5py (tested on 2.5.0)
  • phconvert 0.8 (or later)

These packages depends on yaml (C library), pytables, hdf5 (C library). The installation through conda will automatically install the dependencies.

Feedback

For questions or comments please:

License

phforge is released under the open source MIT license.

Acknowledgements

This work was supported by NIH Grant R01-GM95904.