Interfaces

Python interfaces to HDF5 include h5py and pytables (for which the module name is tables). While we actively use and support h5py, we will not discuss pytables.

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Here is an example of how one might work with vlen data. An example of vlen data is the EvrData. During each event, the EvrData includes fifoCodes - this is a variable length list. Each element in the list has three parts, timestampHigh, timestampLow and eventCode. A lot of users will need to examine the eventCode. Let's. Starting with EvrData::DataV4, one can access event codes without working with vlen data - one uses the dataset 'present' that has been translated into the hdf5. However we want to demonstrate how to work with vlen data. So let's write an example that takes the EvrData and flattens it out into a table, where each entry in the table is 0 or 1 depending on whether or not that eventCode fired (this is exactly the content of the 'present' dataset in the hdf5).

import h5py
import numpy as np

f=h5py.File('/reg/d/psdm/xpp/xpptut13/hdf5/xpptut13-r0179.h5','r')
evrData=f['/Configure:0000/Run:0000/CalibCycle:0000/EvrData::DataV3/NoDetector.0:Evr.0/data']
numberOfEvents = len(evrData)    # this gives 483
largestEventCode = max([max([fifoEvent['eventCode'] for fifoEvent in fifoEvents]) for fifoEvents in  evrData['fifoEvents']])
# this gives 162, this is the largest eventCode that occurs in this calib cycle.
eventCodes = np.zeros((numberOfEvents, largestEventCode+1), np.int8)
for eventIndex,fifoEvents in enumerate(evrData['fifoEvents']):
    for fifoEvent in fifoEvents:
        eventCodes[eventIndex, fifoEvent['eventCode']]=1

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