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Phforge

A script to create Photon-HDF5 files.

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phforge

What is it?

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

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 save a temporary HDF5 containing only the photon-data arrays (timestamps, detectors, nanotimes, etc...) and to generate (or ask the user to write) a YAML file with the metadata (i.e. 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.

Next, the program can invoke phforge script to create a Photon-HDF5 file:

phforge metadata_file hdf5_file out_file

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

How to install?

We provided conda packages for Windows x64 and OS X for both python 3.4 and legacy python 2.7. To install the conda package type:

conda install phforge -c tritemio

A conda installation is required (use either Anaconda or Miniconda3). The installation adds the phforge to the system path so that it can be directly called from any shell.

Alternatively the script can be installed with PIP on any platform.

Dependencies

These packages depends on yaml (C library), pytables 3.2, hdf5 (C library).

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.