Page History

...

Currently LCLS does not offer a an uniform approach to the analysis of accumulated experemental data. Users exploit myana, pyana, MatLab, IDL, CASS, and probably something else. The work on long-awaited project of psana is in progress. The psana is going to be quite generic and probably not so simple approach. In this page we discuss a simple but absolutly flexible approach to analysis of data stored in HDF5 files. It is based on Python code with extensive exploitation of standard libraries. A few examples of how to access and process data are presented at the end of this page.

...

    print 'arr1ev.shape =', arr1ev.shape
    print 'arr1ev =\n',     arr1ev

Advanced operations

Get item attributes

Get group name and the list of daughters

Check if the HDF5 item is "File", "Group", or "Data"

Extract time

Time variable is stored in HDF5 as a tuple of two long integer numbers representing the seconds since 01/01/1970 and nanoseconds as a fraction of the second. Time can be stored in the group attributes and in the data record with name "time", which can be extracted as shown below

• from the group attributes

  Code Block
  group = file["/Configure:0000"] time_sec = group.attrs.values()[0] time_nsec = group.attrs.values()[1]

• from the time data record

  Code Block
  time_dataset = file['/Configure:0000/Run:0000/CalibCycle:0002/Acqiris::DataDescV1/XppLas.0:Acqiris.0/time'] index = 0 # this is an index in the dataset time = time_dataset[index] # get the time tuple consisting of seconds and nanoseconds time_sec = time[0] time_nsec = time[1]

Code examples

Example 1, basic operations:

#!/usr/bin/env python

import h5py
import numpy as np

eventNumber = 5

file    = h5py.File('/reg/d/psdm/XPP/xppcom10/hdf5/xppcom10-r0546.h5', 'r')
dataset = file['/Configure:0000/Run:0000/CalibCycle:0000/Camera::FrameV1/XppSb4Pim.1:Tm6740.1/image']
arr1ev  = dataset[eventNumber]
file.close()

print 'arr1ev.shape =', arr1ev.shape
print 'arr1ev =\n',     arr1ev

Example 2, advanced operations:

Needs to be added

Example, extract and print the time variables:

#!/usr/bin/env python

import h5py
import time

#-----------------------------------------------------

def print_time(t_sec, t_nsec):
    """Converts seconds in human-readable time and prints formatted time"""

    tloc = time.localtime(t_sec) # converts sec to the tuple struct_time in local
    print 'Input time :',t_sec,'sec,',  t_nsec,'nsec, '
    print 'Local time :', time.strftime('%Y-%m-%d %H:%M:%S',tloc)

#-----------------------------------------------------

file_name = '/reg/d/psdm/xpp/xpp22510/hdf5/xpp22510-r0100.h5'
file = h5py.File(file_name, 'r') # open read-only

print "EXAMPLE: Get time from the group attributes:"

group = file["/Configure:0000"]
t_sec  = group.attrs.values()[0]
t_nsec = group.attrs.values()[1]
print_time(t_sec, t_nsec)


print "EXAMPLE: Get time from the data record 'time':"

dataset = file['/Configure:0000/Run:0000/CalibCycle:0002/Acqiris::DataDescV1/XppLas.0:Acqiris.0/time']
index = 0
time = dataset[ind]
t_sec  = time[0]
t_nsec = time[1]
print_time(t_sec, t_nsec)

f.close()

#----------------------------------------------------