Write data to HDF5 file

Question

I'm trying to write data into a HDF5 file using the script below.

The terminal window I'm running the code in gives the correct output, and the output HDF5 file is created, but no data in the tables of the output file.

Any hints?

import tables
import datetime
import time
import csv
from tables import openFile, IsDescription, Float64Col, Int16Col
from scipy import array
import numpy as np
import os

#
output_filename='events_per_hour_output.h5'
#

if __name__ == '__main__':
    # Read data from file
    input_file='data_s20002_20121101_20121105.h5'
#Find station ID, start date and stop date from filename
    print "input_file: ",str(input_file)
    stationID=str(input_file[6:11])
    print "stationID: ",stationID
    start_year=str(input_file[12:16])
    print "start_year: ", start_year
    start_month=str(input_file[16:18])
    print "start_month: ", start_month
    start_day=str(input_file[18:20])
    print "start_day",start_day
    stop_year=str(input_file[21:25])
    print "stop_year ",stop_year
    stop_month=str(input_file[25:27])
    print "stop_month ",stop_month
    stop_day=str(input_file[27:29])
    print "stop_day ",stop_day
    print ''

    with tables.openFile(str(input_file), 'r') as datafile:
           data = [(x['timestamp'], x['nanoseconds'], x['ext_timestamp'], x['pulseheights']) for
                    x in datafile.root.s20002.events]


#
class variable_01(IsDescription):
 unix_timestamp = Float64Col()
 events = Float64Col()
 GMT = Float64Col()
 step = Float64Col()
#
#
start_date=datetime.datetime(int(start_year),int(start_month),int(start_day))
print "start_date: ",start_date
#start_date=time.gmtime(int(start_year),int(start_month),int(start_day))
stop_date=datetime.datetime(int(stop_year),int(stop_month),int(stop_day))
print "stop_date: ",stop_date
print"start_date.timetuple(): ",start_date.timetuple()
start_unix_time=time.mktime(start_date.timetuple())
#start_unix_time=time.gmtime(start_date.timetuple())
stop_unix_time=time.mktime(stop_date.timetuple())
step_length=3600# 3600 seconds = 1 hour
total_length=0
#
with openFile(output_filename, 'w') as data_splice:
            group_variable_01 = data_splice.createGroup("/", 'hisparc_vantage')
            table_variable_01 = data_splice.createTable(group_variable_01, 'table_01', variable_01)
            dummy_01 = table_variable_01.row

#
for hour_step in range(int(start_unix_time),int(stop_unix_time),step_length):
 dummy_01['step']=1
 dummy_01.append

 result = []
 for row in data:
     if (hour_step <= row[0]) and (row[0] < hour_step+step_length):# 
      result.append(row) 
 print "UTC start time: ",time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime(hour_step))
 print "len(result) : ", len(result)
#
#

 dummy_01['unix_timestamp'] = hour_step
 dummy_01['events']=len(result)
 print "dummy_01['events']=",dummy_01['events']
 print "dummy_01['unix_timestamp'] =", dummy_01['unix_timestamp']
 dummy_01.append()
 print ''
table_variable_01.flush
print "Done."

If this is not a duplicate of your other question [Python - problems writing data to HDF5](http://stackoverflow.com/questions/16639813/python-problems-writing-data-to-hdf5) which was closed, you had better explain how. — High Performance Mark, May 20 '13 at 14:15

score 1 · Answer 1 · answered May 20 '13 at 14:04

1

You should take a look at h5py. This module provides very easy functions to read/write HDF5 files. If you read data fields such as images or rasters, there will be directly available as numpy arrays.

answered May 20 '13 at 14:04

Iñigo Hernáez Corres

710
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15

score 0 · Answer 2 · edited May 23 '17 at 12:33

0

import h5py

# Create random data
import numpy as np
data_matrix = np.random.uniform(-1, 1, size=(10, 3))

# Write data to HDF5
data_file = h5py.File('file.hdf5', 'w')
data_file.create_dataset('group_name', data=data_matrix)
data_file.close()

See also: How to read HDF5 files in Python

edited May 23 '17 at 12:33

Community

1
1

answered Jan 11 '17 at 09:11

Martin Thoma

124,992
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Write data to HDF5 file

2 Answers2