what is a fast way to output h5py dataset to text?
- by user362761
I am using the h5py python package to read files in HDF5 format. (e.g. somefile.h5)
I would like to write the contents of a dataset to a text file.
For example, I would like to create a text file with the following contents:
1,20,31,75,142,324,78,12,3,90,8,21,1
I am able to access the dataset in python using this code:
import h5py
f = h5py.File('/Users/Me/Desktop/thefile.h5', 'r')
group = f['/level1/level2/level3']
dset = group['dsetname']
My naive approach is too slow, because my dataset has over 20000 entries:
# write all values to file
for index in range(len(dset)):
# do not add comma after last value
if index == len(dset)-1: txtfile.write(repr(dset[index]))
else: txtfile.write(repr(dset[index])+',')
txtfile.close()
return None
Is there a faster way to write this to a file? Perhaps I could convert the dataset into a NumPy array or even a Python list, and then use some file-writing tool?
(I could experiment with concatenating the values into a larger string before writing to file, but I'm hoping there's something entirely more elegant)
