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.. basic_data_io:
===============
Basic Data IO
===============
Accessing images using nipy:
While Nifti_ is the primary file format Analyze images (with associated .mat
file), and MINC files can also be read.
Load Image from File
====================
Get a filename for an example file. ``anatfile`` gives a filename for a small
testing image in the nipy distribution:
>>> from nipy.testing import anatfile
Load the file from disk:
>>> from nipy import load_image
>>> myimg = load_image(anatfile)
>>> myimg.shape
(33, 41, 25)
>>> myimg.affine
array([[ -2., 0., 0., 32.],
[ 0., 2., 0., -40.],
[ 0., 0., 2., -16.],
[ 0., 0., 0., 1.]])
Access Data into an Array
=========================
This allows the user to access data as a numpy array.
>>> mydata = myimg.get_fdata()
>>> mydata.shape
(33, 41, 25)
>>> mydata.ndim
3
Save image to a File
====================
>>> from nipy import save_image
>>> newimg = save_image(myimg, 'newmyfile.nii')
Create Image from an Array
===========================
This will have a generic affine-type CoordinateMap with unit voxel sizes.
>>> import numpy as np
>>> from nipy.core.api import Image, vox2mni
>>> rawarray = np.zeros((43,128,128))
>>> arr_img = Image(rawarray, vox2mni(np.eye(4)))
>>> arr_img.shape
(43, 128, 128)
Coordinate map
==============
Images have a Coordinate Map.
The Coordinate Map contains information defining the input (domain) and output
(range) Coordinate Systems of the image, and the mapping between the two
Coordinate systems. The *input* coordinate system is the *voxel* coordinate
system, and the *output* coordinate system is the *world* coordinate system.
>>> newimg.coordmap
AffineTransform(
function_domain=CoordinateSystem(coord_names=('i', 'j', 'k'), name='voxels', coord_dtype=float64),
function_range=CoordinateSystem(coord_names=('aligned-x=L->R', 'aligned-y=P->A', 'aligned-z=I->S'), name='aligned', coord_dtype=float64),
affine=array([[ -2., 0., 0., 32.],
[ 0., 2., 0., -40.],
[ 0., 0., 2., -16.],
[ 0., 0., 0., 1.]])
)
See :ref:`coordinate_map` for more detail.
.. testcleanup::
# Delete the file we wrote out further up the page.
import os
os.unlink('newmyfile.nii')
.. include:: ../links_names.txt
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