/usr/lib/python2.7/dist-packages/dipy/io/utils.py is in python-dipy 0.10.1-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | ''' Utility functions for file formats '''
from __future__ import division, print_function, absolute_import
import numpy as np
from nibabel import Nifti1Image
def nifti1_symmat(image_data, *args, **kwargs):
"""Returns a Nifti1Image with a symmetric matrix intent
Parameters:
-----------
image_data : array-like
should have lower triangular elements of a symmetric matrix along the
last dimension
all other arguments and keywords are passed to Nifti1Image
Returns:
--------
image : Nifti1Image
5d, extra dimensions addes before the last. Has symmetric matrix intent
code
"""
image_data = make5d(image_data)
last_dim = image_data.shape[-1]
n = (np.sqrt(1+8*last_dim) - 1)/2
if (n % 1) != 0:
raise ValueError("input_data does not seem to have matrix elements")
image = Nifti1Image(image_data, *args, **kwargs)
hdr = image.get_header()
hdr.set_intent('symmetric matrix', (n,))
return image
def make5d(input):
"""reshapes the input to have 5 dimensions, adds extra dimensions just
before the last dimession
"""
input = np.asarray(input)
if input.ndim > 5:
raise ValueError("input is already more than 5d")
shape = input.shape
shape = shape[:-1] + (1,)*(5-len(shape)) + shape[-1:]
return input.reshape(shape)
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