I have a complex type h5 file. 2d array. I want to imshow it. But I have following error. What is wrong?
import h5py
import numpy as np
import matplotlib.pyplot as plt
with h5py.File('obj_0001.h5', 'r') as hdf:
ls = list(hdf.keys())
print('List of datasets in thies file: \n', ls)
data = hdf.get('dataset')
diff = np.array(data)
print('Shape of dataset: \n', diff.shape)
plt.figure(1)
plt.imshow(np.abs(diff))
plt.savefig('diff_test.png')
plt.show()
UFuncTypeError: ufunc 'absolute' did not contain a loop with signature matching types dtype([('real', '<f4'), ('imag', '<f4')]) -> dtype([('real', '<f4'), ('imag', '<f4')])
According to http://docs.h5py.org/en/stable/faq.html#what-datatypes-are-supported
h5py supports complex dtype, representing a HDF5 struc.
The error indicates diff.dtype is dtype([('real', '<f4'), ('imag', '<f4')]). I don't know if that is the result of your np.array(data) conversion or there's something different about how the data is stored on the file.
diff = data[:]
might be worth trying, since that's the preferred syntax for loading an array from a dataset.
But if diff is that structured array, you can make a complex dtype with:
In [303]: arr2 = np.ones((3,), np.dtype([('real','f'),('imag','f')]))
In [304]: arr2
Out[304]:
array([(1., 1.), (1., 1.), (1., 1.)],
dtype=[('real', '<f4'), ('imag', '<f4')])
In [305]: arr3 = arr2['real']+1j*arr2['imag']
In [306]: arr3
Out[306]: array([1.+1.j, 1.+1.j, 1.+1.j], dtype=complex64)
testing in abs:
In [307]: np.abs(arr2)
---------------------------------------------------------------------------
UFuncTypeError Traceback (most recent call last)
<ipython-input-307-333e28818b26> in <module>
----> 1 np.abs(arr2)
UFuncTypeError: ufunc 'absolute' did not contain a loop with signature matching types dtype([('real', '<f4'), ('imag', '<f4')]) -> dtype([('real', '<f4'), ('imag', '<f4')])
In [308]: np.abs(arr3)
Out[308]: array([1.4142135, 1.4142135, 1.4142135], dtype=float32)