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Add the mode param for border management. #364

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May 26, 2014
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87 changes: 50 additions & 37 deletions dipy/align/aniso2iso.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,15 @@
import numpy as np
from scipy.ndimage import affine_transform

def resample(data,affine,zooms,new_zooms,order=1):
''' Resample data from anisotropic to isotropic voxel size


def resample(data, affine, zooms, new_zooms, order=1, mode='constant', cval=0):
"""Resample data from anisotropic to isotropic voxel size

Parameters
----------
data : array, shape (I,J,K) or (I,J,K,N)
data : array, shape (I,J,K) or (I,J,K,N)
3d volume or 4d volume with datasets
affine : array, shape (4,4)
affine : array, shape (4,4)
mapping from voxel coordinates to world coordinates
zooms : tuple, shape (3,)
voxel size for (i,j,k) dimensions
Expand All @@ -20,57 +21,69 @@ def resample(data,affine,zooms,new_zooms,order=1):
order of interpolation for resampling/reslicing,
0 nearest interpolation, 1 trilinear etc..
if you don't want any smoothing 0 is the option you need.

mode : string ('constant', 'nearest', 'reflect' or 'wrap')
Points outside the boundaries of the input are filled according
to the given mode.
cval : float
Value used for points outside the boundaries of the input if
mode='constant'.

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If you add mode, I guess one should also add cval.

Returns
-------
data2 : array, shape (I,J,K) or (I,J,K,N)
data2 : array, shape (I,J,K) or (I,J,K,N)
datasets resampled into isotropic voxel size
affine2 : array, shape (4,4)
new affine for the resampled image

Notes
-----
It is also possible with this function to resample/reslice from isotropic voxel size to anisotropic
or from isotropic to isotropic or even from anisotropic to anisotropic, as long as you provide
the correct zooms (voxel sizes) and new_zooms (new voxel sizes). It is fairly easy to get the correct
zooms using nibabel as show in the example below.

It is also possible with this function to resample/reslice from isotropic
voxel size to anisotropic or from isotropic to isotropic or even from
anisotropic to anisotropic, as long as you provide the correct zooms
(voxel sizes) and new_zooms (new voxel sizes). It is fairly easy to get the
correct zooms using nibabel as show in the example below.

Examples
--------
>>> import nibabel as nib
>>> from dipy.align.aniso2iso import resample
>>> from dipy.data import get_data
>>> fimg=get_data('aniso_vox')
>>> img=nib.load(fimg)
>>> data=img.get_data()
>>> from dipy.data import get_data
>>> fimg = get_data('aniso_vox')
>>> img = nib.load(fimg)
>>> data = img.get_data()
>>> data.shape
(58, 58, 24)
>>> affine=img.get_affine()
>>> zooms=img.get_header().get_zooms()[:3]
>>> zooms
>>> affine = img.get_affine()
>>> zooms = img.get_header().get_zooms()[:3]
>>> zooms
(4.0, 4.0, 5.0)
>>> new_zooms=(3.,3.,3.)
>>> new_zooms = (3.,3.,3.)
>>> new_zooms
(3.0, 3.0, 3.0)
>>> data2,affine2=resample(data,affine,zooms,new_zooms)
>>> data2, affine2 = resample(data, affine, zooms, new_zooms)
>>> data2.shape
(77, 77, 40)

'''
R=np.diag(np.array(new_zooms)/np.array(zooms))
new_shape=np.array(zooms)/np.array(new_zooms) * np.array(data.shape[:3])
new_shape=np.round(new_shape).astype('i8')
if data.ndim==3:
data2=affine_transform(input=data,matrix=R,offset=np.zeros(3,),output_shape=tuple(new_shape),order=order)
if data.ndim==4:
"""
R = np.diag(np.array(new_zooms)/np.array(zooms))
new_shape = np.array(zooms)/np.array(new_zooms) * np.array(data.shape[:3])
new_shape = np.round(new_shape).astype('i8')
if data.ndim == 3:
data2 = affine_transform(input=data, matrix=R, offset=np.zeros(3,),
output_shape=tuple(new_shape),
order=order, mode=mode, cval=cval)
if data.ndim == 4:
data2l=[]
for i in range(data.shape[-1]):
tmp=affine_transform(input=data[...,i],matrix=R,offset=np.zeros(3,),output_shape=tuple(new_shape),order=order)
tmp = affine_transform(input=data[..., i], matrix=R,
offset=np.zeros(3,),
output_shape=tuple(new_shape),
order=order, mode=mode, cval=cval)
data2l.append(tmp)
data2=np.zeros(tmp.shape+(data.shape[-1],),data.dtype)
data2 = np.zeros(tmp.shape+(data.shape[-1],), data.dtype)
for i in range(data.shape[-1]):
data2[...,i]=data2l[i]
Rx=np.eye(4)
Rx[:3,:3]=R
affine2=np.dot(affine,Rx)
return data2,affine2
data2[..., i] = data2l[i]

Rx = np.eye(4)
Rx[:3, :3] = R
affine2 = np.dot(affine, Rx)
return data2, affine2