-
Notifications
You must be signed in to change notification settings - Fork 16
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
feat: split transform chains out from base and add a load function
This was necessary to integrate one test equivalent to resampling with ``antsApplyTransforms``, but via nitransforms.
- Loading branch information
Showing
5 changed files
with
234 additions
and
141 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*- | ||
| # vi: set ft=python sts=4 ts=4 sw=4 et: | ||
| ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## | ||
| # | ||
| # See COPYING file distributed along with the NiBabel package for the | ||
| # copyright and license terms. | ||
| # | ||
| ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## | ||
| """Common interface for transforms.""" | ||
| from collections.abc import Iterable | ||
|
|
||
| from .base import ( | ||
| TransformBase, | ||
| TransformError, | ||
| ) | ||
| from .linear import Affine | ||
| from .nonlinear import DisplacementsFieldTransform | ||
|
|
||
|
|
||
| class TransformChain(TransformBase): | ||
| """Implements the concatenation of transforms.""" | ||
|
|
||
| __slots__ = ('_transforms', ) | ||
|
|
||
| def __init__(self, transforms=None): | ||
| """Initialize a chain of transforms.""" | ||
| super().__init__() | ||
| self._transforms = None | ||
|
|
||
| if transforms is not None: | ||
| self.transforms = transforms | ||
|
|
||
| def __add__(self, b): | ||
| """ | ||
| Compose this and other transforms. | ||
| Example | ||
| ------- | ||
| >>> T1 = TransformBase() | ||
| >>> added = T1 + TransformBase() + TransformBase() | ||
| >>> isinstance(added, TransformChain) | ||
| True | ||
| >>> len(added.transforms) | ||
| 3 | ||
| """ | ||
| self.append(b) | ||
| return self | ||
|
|
||
| def __getitem__(self, i): | ||
| """ | ||
| Enable indexed access of transform chains. | ||
| Example | ||
| ------- | ||
| >>> T1 = TransformBase() | ||
| >>> chain = T1 + TransformBase() | ||
| >>> chain[0] is T1 | ||
| True | ||
| """ | ||
| return self.transforms[i] | ||
|
|
||
| def __len__(self): | ||
| """Enable using len().""" | ||
| return len(self.transforms) | ||
|
|
||
| @property | ||
| def transforms(self): | ||
| """Get the internal list of transforms.""" | ||
| return self._transforms | ||
|
|
||
| @transforms.setter | ||
| def transforms(self, value): | ||
| self._transforms = _as_chain(value) | ||
| if self.transforms[-1].reference: | ||
| self.reference = self.transforms[-1].reference | ||
|
|
||
| def append(self, x): | ||
| """ | ||
| Concatenate one element to the chain. | ||
| Example | ||
| ------- | ||
| >>> chain = TransformChain(transforms=TransformBase()) | ||
| >>> chain.append((TransformBase(), TransformBase())) | ||
| >>> len(chain) | ||
| 3 | ||
| """ | ||
| self.transforms += _as_chain(x) | ||
|
|
||
| def insert(self, i, x): | ||
| """ | ||
| Insert an item at a given position. | ||
| Example | ||
| ------- | ||
| >>> chain = TransformChain(transforms=[TransformBase(), TransformBase()]) | ||
| >>> chain.insert(1, TransformBase()) | ||
| >>> len(chain) | ||
| 3 | ||
| >>> chain.insert(1, TransformChain(chain)) | ||
| >>> len(chain) | ||
| 6 | ||
| """ | ||
| self.transforms = self.transforms[:i] + _as_chain(x) + self.transforms[i:] | ||
|
|
||
| def map(self, x, inverse=False): | ||
| """ | ||
| Apply a succession of transforms, e.g., :math:`y = f_3(f_2(f_1(f_0(x))))`. | ||
| Example | ||
| ------- | ||
| >>> chain = TransformChain(transforms=[TransformBase(), TransformBase()]) | ||
| >>> chain([(0., 0., 0.), (1., 1., 1.), (-1., -1., -1.)]) | ||
| [(0.0, 0.0, 0.0), (1.0, 1.0, 1.0), (-1.0, -1.0, -1.0)] | ||
| >>> chain([(0., 0., 0.), (1., 1., 1.), (-1., -1., -1.)], inverse=True) | ||
| [(0.0, 0.0, 0.0), (1.0, 1.0, 1.0), (-1.0, -1.0, -1.0)] | ||
| >>> TransformChain()((0., 0., 0.)) # doctest: +IGNORE_EXCEPTION_DETAIL | ||
| Traceback (most recent call last): | ||
| TransformError: | ||
| """ | ||
| if not self.transforms: | ||
| raise TransformError('Cannot apply an empty transforms chain.') | ||
|
|
||
| transforms = self.transforms | ||
| if not inverse: | ||
| transforms = self.transforms[::-1] | ||
|
|
||
| for xfm in transforms: | ||
| x = xfm(x, inverse=inverse) | ||
|
|
||
| return x | ||
|
|
||
| @classmethod | ||
| def from_filename(cls, filename, fmt="X5", | ||
| reference=None, moving=None): | ||
| """Load a transform file.""" | ||
| from .io import itk | ||
|
|
||
| retval = [] | ||
| if str(filename).endswith(".h5"): | ||
| reference = None | ||
| xforms = itk.ITKCompositeH5.from_filename(filename) | ||
| for xfmobj in xforms: | ||
| if isinstance(xfmobj, itk.ITKLinearTransform): | ||
| retval.append(Affine(xfmobj.to_ras(), reference=reference)) | ||
| else: | ||
| retval.append(DisplacementsFieldTransform(xfmobj)) | ||
|
|
||
| return TransformChain(retval) | ||
|
|
||
| raise NotImplementedError | ||
|
|
||
|
|
||
| def _as_chain(x): | ||
| """Convert a value into a transform chain.""" | ||
| if isinstance(x, TransformChain): | ||
| return x.transforms | ||
| if isinstance(x, Iterable): | ||
| return list(x) | ||
| return [x] | ||
|
|
||
|
|
||
| load = TransformChain.from_filename |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.