__all__ = ['get_orientation',
'reorient_image2',
'get_possible_orientations',
'get_center_of_mass']
import numpy as np
from tempfile import mktemp
from . import apply_transforms
from .. import utils
from ..core import ants_image as iio
_possible_orientations = ['RIP','LIP', 'RSP', 'LSP', 'RIA', 'LIA',
'RSA', 'LSA', 'IRP', 'ILP', 'SRP', 'SLP', 'IRA', 'ILA', 'SRA',
'SLA', 'RPI', 'LPI', 'RAI', 'LAI', 'RPS', 'LPS', 'RAS', 'LAS',
'PRI', 'PLI', 'ARI', 'ALI', 'PRS', 'PLS', 'ARS', 'ALS', 'IPR',
'SPR', 'IAR', 'SAR', 'IPL', 'SPL', 'IAL', 'SAL', 'PIR', 'PSR',
'AIR', 'ASR', 'PIL', 'PSL', 'AIL', 'ASL']
[docs]def get_possible_orientations():
return _possible_orientations
[docs]def get_orientation(image):
direction = image.direction
orientation = []
for i in range(3):
row = direction[:,i]
idx = np.where(np.abs(row)==np.max(np.abs(row)))[0][0]
if idx == 0:
if row[idx] < 0:
orientation.append('L')
else:
orientation.append('R')
elif idx == 1:
if row[idx] < 0:
orientation.append('P')
else:
orientation.append('A')
elif idx == 2:
if row[idx] < 0:
orientation.append('S')
else:
orientation.append('I')
return ''.join(orientation)
[docs]def reorient_image2(image, orientation='RAS'):
"""
Reorient an image.
Example
-------
>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni2 = mni.reorient_image2()
"""
if image.dimension != 3:
raise ValueError('image must have 3 dimensions')
inpixeltype = image.pixeltype
ndim = image.dimension
if image.pixeltype != 'float':
image = image.clone('float')
libfn = utils.get_lib_fn('reorientImage2')
itkimage = libfn(image.pointer, orientation)
new_img = iio.ANTsImage(pixeltype='float', dimension=ndim,
components=image.components, pointer=itkimage)#.clone(inpixeltype)
if inpixeltype != 'float':
new_img = new_img.clone(inpixeltype)
return new_img
[docs]def get_center_of_mass(image):
"""
Compute an image center of mass in physical space which is defined
as the mean of the intensity weighted voxel coordinate system.
ANTsR function: `getCenterOfMass`
Arguments
---------
image : ANTsImage
image from which center of mass will be computed
Returns
-------
scalar
Example
-------
>>> fi = ants.image_read( ants.get_ants_data("r16"))
>>> com1 = ants.get_center_of_mass( fi )
>>> fi = ants.image_read( ants.get_ants_data("r64"))
>>> com2 = ants.get_center_of_mass( fi )
"""
if image.pixeltype != 'float':
image = image.clone('float')
libfn = utils.get_lib_fn('centerOfMass%s' % image._libsuffix)
com = libfn(image.pointer)
return tuple(com)
