def test_labels1():
img = load_image(funcfile)
parcelmap = fromarray(np.asarray(img[0]), 'kji', 'zyx')
parcelmap = (np.asarray(parcelmap) * 100).astype(np.int32)
v = 0
for i, d in fmri_generator(img, parcels(parcelmap)):
v += d.shape[1]
assert_equal(v, parcelmap.size)
def aniso2iso(self, image, spacing, dimensions):
'''
from dipy.align.aniso2iso
'''
header = image.header
oldspacing = header.get_zooms()
olddimensions = image.shape[:3]
if spacing == 'no':
newspacing = (min(oldspacing), min(oldspacing), min(oldspacing))
else:
newspacing = (float(spacing.split(',')[0]),
float(spacing.split(',')[1]),
float(spacing.split(',')[2]))
if dimensions == 'no':
newdimensions = olddimensions
else:
newdimensions = (int(dimensions.split(',')[0]),
int(dimensions.split(',')[1]),
int(dimensions.split(',')[2]))
c.info('Resampling the master image..')
c.info(' old spacing ' + str(oldspacing))
c.info(' old dimensions ' + str(olddimensions))
# work on a numpy array to resample to isotropic spacing
R = numpy.diag(numpy.array(newspacing) / numpy.array(oldspacing))
new_shape = numpy.array(oldspacing) / numpy.array(
newspacing) * numpy.array(newdimensions)
new_shape = numpy.round(new_shape).astype('i8')
newImage = affine_transform(input=image,
matrix=R,
offset=numpy.zeros(3, ),
output_shape=tuple(new_shape),
order=0)
Rx = numpy.eye(4)
Rx[:3, :3] = R
# get the mew world-image matrix
affine = numpy.dot(image.coordmap.affine, Rx)
# convert to NiPy image
# copy the old coordmap and replace the affine matrix
newCoordMap = image.coordmap
newCoordMap.affine = affine
# create a new NiPy image with the resampled data and the new coordmap (including the affine matrix)
nipyImage = fromarray(newImage, '', '', newCoordMap)
c.info(' new spacing ' + str(newspacing))
c.info(' new dimensions ' + str(nipyImage.shape[:3]))
return nipyImage
def uint8_to_dtype(dtype, name):
dtype = dtype
shape = (2,3,4)
dmax = np.iinfo(np.uint8).max
data = np.random.randint(0, dmax, size=shape)
data[0,0,0] = 0
data[1,0,0] = dmax
data = data.astype(np.uint8) # randint returns np.int32
img = fromarray(data, 'kji', 'zxy')
newimg = save_image(img, name, dtype=dtype)
return newimg.get_data(), data
def test_slicing_returns_image():
data = np.ones((2,3,4))
img = fromarray(data, 'kji', 'zyx')
assert isinstance(img, Image)
assert img.ndim == 3
# 2D slice
img2D = img[:,:,0]
assert isinstance(img2D, Image)
assert img2D.ndim == 2
# 1D slice
img1D = img[:,0,0]
assert isinstance(img1D, Image)
assert img1D.ndim == 1
def float32_to_dtype(dtype, name):
# Utility function for the scaling_float32 function
dtype = dtype
shape = (2,3,4)
# set some value value for scaling our data
scale = np.iinfo(np.uint16).max * 2.0
data = np.random.normal(size=(2,3,4), scale=scale)
data[0,0,0] = np.finfo(np.float32).max
data[1,0,0] = np.finfo(np.float32).min
# random.normal will return data as native machine type
data = data.astype(np.float32)
img = fromarray(data, 'kji', 'zyx')
newimg = save_image(img, name, dtype=dtype)
return newimg.get_data(), data
def test_roundtrip_fromarray():
data = np.random.rand(10,20,30)
img = fromarray(data, 'kji', 'xyz')
with InTemporaryDirectory():
save_image(img, 'img.nii.gz')
img2 = load_image('img.nii.gz')
data2 = img2.get_data()
# verify data
assert_almost_equal(data2, data)
assert_almost_equal(data2.mean(), data.mean())
assert_almost_equal(data2.min(), data.min())
assert_almost_equal(data2.max(), data.max())
# verify shape and ndims
assert_equal(img2.shape, img.shape)
assert_equal(img2.ndim, img.ndim)
# verify affine
assert_almost_equal(img2.affine, img.affine)
def test_roundtrip_fromarray():
data = np.random.rand(10,20,30)
img = fromarray(data, 'kji', 'xyz')
fd, name = mkstemp(suffix='.nii.gz')
tmpfile = open(name)
save_image(img, tmpfile.name)
img2 = load_image(tmpfile.name)
data2 = np.asarray(img2)
tmpfile.close()
os.unlink(name)
# verify data
yield assert_true, np.allclose(data2, data)
yield assert_true, np.allclose(data2.mean(), data.mean())
yield assert_true, np.allclose(data2.min(), data.min())
yield assert_true, np.allclose(data2.max(), data.max())
# verify shape and ndims
yield assert_equal, img2.shape, img.shape
yield assert_equal, img2.ndim, img.ndim
# verify affine
yield assert_true, np.allclose(img2.affine, img.affine)
from nipy.core.image import image
from nipy.core.api import Image, fromarray, merge_images, is_image
from nipy.core.api import parcels, data_generator, write_data
from nipy.core.reference.coordinate_map import Affine
from nipy.io.api import load_image
def setup():
# Suppress warnings during tests to reduce noise
warnings.simplefilter("ignore")
def teardown():
# Clear list of warning filters
warnings.resetwarnings()
_data = np.arange(24).reshape((4,3,2))
gimg = fromarray(_data, 'ijk', 'xyz')
def test_init():
new = Image(np.asarray(gimg), gimg.coordmap)
yield assert_array_almost_equal, np.asarray(gimg), np.asarray(new)
yield assert_raises, ValueError, Image, None, None
def test_maxmin_values():
y = np.asarray(gimg)
yield assert_equal, y.shape, tuple(gimg.shape)
yield assert_equal, y.max(), 23
yield assert_equal, y.min(), 0.0
# Specify the axis order of the input coordinates
input_coords = ['k', 'j', 'i']
output_coords = ['z','y','x']
#or
innames = ('kji')
outnames = ('zyx')
# either way works
# Build a CoordinateMap to create the image with
affine_coordmap = Affine.from_params(innames, outnames, affine_array)
# 2) Create a nipy image from the array and CoordinateMap
# Create new image
newimg = fromarray(arr, innames=innames, outnames=outnames,
coordmap=affine_coordmap)
################################################################################
# END HERE, for testing purposes only.
################################################################################
# Imports used just for development and testing. Users typically
# would not uses these when creating an image.
from tempfile import mkstemp
from nipy.testing import assert_equal
# We use a temporary file for this example so as to not create junk
# files in the nipy directory.
fd, name = mkstemp(suffix='.nii.gz')
tmpfile = open(name)
# Save the nipy image to the specified filename
"""This example shows how to create a temporary image to use during processing.
The array is filled with zeros.
"""
import numpy as np
from nipy.core.api import fromarray, save_image
# create an array of zeros, the shape of your data array
zero_array = np.zeros((91,109,91))
# create an image from our array
img = fromarray(zero_array)
# save the image to a file
newimg = save_image(img, 'tempimage.nii.gz')
# Example of creating a temporary image file from an existing image
# with a matching comap.
# from nipy.core.api import load_image
# img = load_image('foo.nii.gz')
# zeroarray = np.zeros(img.comap.shape)
# zeroimg = fromarray(zeroarray, comap=img.comap)
# newimg = save_image(zeroimg, 'tempimage.nii.gz')