如何使用 h5py 读取 Row Wise 而不是 column wise？

Question

I have this matlab file that is of shape 70x10,000,000 (10,000,000 columns 70 rows) Whats annoying is that when I run this line of code which is supposed to print that chunk of data,

f = h5py.File(filepath, 'r')
item = list(f.items())[0][1]
print(item)

it reshapes it into 10,000,000x70 (10,000,000 rows, 70 columns) Is there a way to keep the original shape?

Answer 1

h5py returns HDF5 data as Numpy arrays. So, the key to using h5py is using Numpy methods when needed. You can easily transpose an array using np.transpose() . A simple example is provided below. It creates a HDF5 file with 2 datasets: 1) an array with shape (20,5), and 2) the transposed array with shape (5,20). Then it extracts the 2 arrays and uses np.transpose() to switch row/column order.

with h5py.File('SO_67031436','w') as h5w:
    arr = np.arange(100.).reshape(20,5)
    h5w.create_dataset('ds_1',data=arr)
    h5w.create_dataset('ds_1t',data=np.transpose(arr))
    
with h5py.File('SO_67031436','r') as h5r:
    for name in h5r:
        print(name,',shape=',h5r[name].shape)
        arr=np.transpose(h5r[name][:])
        print('transposed shape=',arr.shape)