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where item stands for file, group of dataset.
Check if the HDF5 item is "File", "Group", or "
...
Dataset"
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isFile = isinstance(item, h5py.File) isGroup = isinstance(item, h5py.Group) isDataset = isinstance(item, h5py.Dataset) |
In this example the standard Python method isinstance(...)}} returns {{True or False in each case, respectively.
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- Get item attributes for File or Group (if attributes available)
In this example theitemmight be a group or fileCode Block item.attrs # for example: <Attributes of HDF5 object at 230141696> item.attrs.keys() # for example: ['start.seconds', 'start.nanoseconds'] item.attrs.values() # for example: [1297608424L, 627075857L] len(item.attrs) #
For
...
example,
...
one
...
of
...
the
...
file
...
attributes
...
is
...
a
...
run
...
number
...
,
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run_number = file.attrs['runNumber']
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- Get the list of daughters in the
group
or convert the group in dictinary and iterate over their key and values,Code Block list_of_item_names = group.items() print list_of_item_names
Code Block for key,val in dict(group).iteritems(): print key, val
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- from the
timedata recordCode 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
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: basic operations
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#!/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
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Example 2
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: advanced operations
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Extract and print the time variables:
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#!/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()
#----------------------------------------------------
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...
Print entire file/group structure using recursive method
| Code Block |
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#!/usr/bin/env python
import h5py
def print_group(g,offset=' '):
"""Prints the input file/group/dataset (g) name and begin iterations on its content"""
print "Structure of the",
if isinstance(g,h5py.File): print "'File'",
elif isinstance(g,h5py.Group): print "'Group' from file",
elif isinstance(g,h5py.Dataset): print "'Dataset' from file",
print g.file,"\n",g.name
if isinstance(g,h5py.Dataset): print offset, "(Dateset) len =", g.shape #, subg.dtype
else: print_group_content(g,offset)
def print_group_content(g,offset=' '):
"""Prints content of the file/group/dataset iteratively, starting from the sub-groups of g"""
for key,val in dict(g).iteritems():
subg = val
print offset, key, #," ", subg.name #, val, subg.len(), type(subg),
if isinstance(subg, h5py.Dataset):
print " (Dateset) len =", subg.shape #, subg.dtype
elif isinstance(subg, h5py.Group):
print " (Group) len =",len(subg)
print_group_content(subg,offset + ' ')
def print_hdf5_file_structure(file_name):
"""Prints the HDF5 file structure"""
file = h5py.File(file_name, 'r') # open read-only
print_group(file)
file.close()
print '=== EOF ==='
if __name__ == "__main__" :
print_hdf5_file_structure('/reg/d/psdm/xpp/xpp22510/hdf5/xpp22510-r0100.h5')
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