The io.files module provides basic functions for working with file-based images in nipy.
See documentation for load and save functions for worked examples.
Load image from filename or pass through image instance
Parameters: | image_input : str or Image instance
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Returns: | img : Image or Image-like instance
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Raises: | TypeError : if neither string nor image-like passed |
Examples
>>> from nipy.testing import anatfile
>>> from nipy.io.api import load_image
>>> img = as_image(anatfile)
>>> img2 = as_image(img)
>>> img2 is img
True
Load an image from the given filename.
Parameters: | filename : string
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Returns: | image : An Image object
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See also
Examples
>>> from nipy.io.api import load_image
>>> from nipy.testing import anatfile
>>> img = load_image(anatfile)
>>> img.shape
(33, 41, 25)
Write the image to a file.
Parameters: | img : An Image object filename : string
dtype_from : {‘data’, ‘header’} or dtype specifier, optional
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Returns: | image : An Image object
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See also
Notes
Filetype is determined by the file extension in ‘filename’. Currently the following filetypes are supported:
Examples
Make a temporary directory to store files
>>> import os
>>> from tempfile import mkdtemp
>>> tmpdir = mkdtemp()
Make some some files and save them
>>> import numpy as np
>>> from nipy.core.api import Image, AffineTransform
>>> from nipy.io.api import save_image
>>> data = np.zeros((91,109,91), dtype=np.uint8)
>>> cmap = AffineTransform('kji', 'zxy', np.eye(4))
>>> img = Image(data, cmap)
>>> fname1 = os.path.join(tmpdir, 'img1.nii.gz')
>>> saved_img1 = save_image(img, fname1)
>>> saved_img1.shape
(91, 109, 91)
>>> fname2 = os.path.join(tmpdir, 'img2.img.gz')
>>> saved_img2 = save_image(img, fname2)
>>> saved_img2.shape
(91, 109, 91)
>>> fname = 'test.mnc'
>>> saved_image3 = save_image(img, fname)
Traceback (most recent call last):
...
ValueError: Sorry, we cannot yet save as format "minc"
Traceback (most recent call last):
...
ValueError: Sorry, we cannot yet save as format "minc"
Finally, we clear up our temporary files:
>>> import shutil
>>> shutil.rmtree(tmpdir)