From fbc92284642a003ad8bdcd66e616070e1143abb0 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 20 Jul 2022 17:04:59 +0200
Subject: [PATCH] ENH: Collapse linear and nonlinear transforms chains
Very undertested, but currently there is a test that uses a "collapsed"
transform on an ITK's .h5 file with one affine and one nonlinear.
BSpline transforms not currently supported.
Resolves #89.
---
nitransforms/linear.py | 16 +++++++---------
nitransforms/manip.py | 16 +++++++---------
nitransforms/tests/test_linear.py | 6 +++---
nitransforms/tests/test_manip.py | 8 +++++++-
4 files changed, 24 insertions(+), 22 deletions(-)
diff --git a/nitransforms/linear.py b/nitransforms/linear.py
index 9c430d3b..239f0ebc 100644
--- a/nitransforms/linear.py
+++ b/nitransforms/linear.py
@@ -123,19 +123,17 @@ def __matmul__(self, b):
True
>>> xfm1 = Affine([[1, 0, 0, 4], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]])
- >>> xfm1 @ np.eye(4) == xfm1
+ >>> xfm1 @ Affine() == xfm1
True
"""
- if not isinstance(b, self.__class__):
- _b = self.__class__(b)
- else:
- _b = b
+ if isinstance(b, self.__class__):
+ return self.__class__(
+ b.matrix @ self.matrix,
+ reference=b.reference,
+ )
- retval = self.__class__(self.matrix.dot(_b.matrix))
- if _b.reference:
- retval.reference = _b.reference
- return retval
+ return b @ self
@property
def matrix(self):
diff --git a/nitransforms/manip.py b/nitransforms/manip.py
index 233f5adf..58d15058 100644
--- a/nitransforms/manip.py
+++ b/nitransforms/manip.py
@@ -8,7 +8,6 @@
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Common interface for transforms."""
from collections.abc import Iterable
-import numpy as np
from .base import (
TransformBase,
@@ -140,9 +139,9 @@ def map(self, x, inverse=False):
return x
- def asaffine(self, indices=None):
+ def collapse(self):
"""
- Combine a succession of linear transforms into one.
+ Combine a succession of transforms into one.
Example
------
@@ -150,7 +149,7 @@ def asaffine(self, indices=None):
... Affine.from_matvec(vec=(2, -10, 3)),
... Affine.from_matvec(vec=(-2, 10, -3)),
... ])
- >>> chain.asaffine()
+ >>> chain.collapse()
array([[1., 0., 0., 0.],
[0., 1., 0., 0.],
[0., 0., 1., 0.],
@@ -160,7 +159,7 @@ def asaffine(self, indices=None):
... Affine.from_matvec(vec=(1, 2, 3)),
... Affine.from_matvec(mat=[[0, 1, 0], [0, 0, 1], [1, 0, 0]]),
... ])
- >>> chain.asaffine()
+ >>> chain.collapse()
array([[0., 1., 0., 2.],
[0., 0., 1., 3.],
[1., 0., 0., 1.],
@@ -168,7 +167,7 @@ def asaffine(self, indices=None):
>>> np.allclose(
... chain.map((4, -2, 1)),
- ... chain.asaffine().map((4, -2, 1)),
+ ... chain.collapse().map((4, -2, 1)),
... )
True
@@ -178,9 +177,8 @@ def asaffine(self, indices=None):
The indices of the values to extract.
"""
- affines = self.transforms if indices is None else np.take(self.transforms, indices)
- retval = affines[0]
- for xfm in affines[1:]:
+ retval = self.transforms[-1]
+ for xfm in reversed(self.transforms[:-1]):
retval = xfm @ retval
return retval
diff --git a/nitransforms/tests/test_linear.py b/nitransforms/tests/test_linear.py
index eea77b7f..f3f83b38 100644
--- a/nitransforms/tests/test_linear.py
+++ b/nitransforms/tests/test_linear.py
@@ -372,10 +372,10 @@ def test_mulmat_operator(testdata_path):
mat2 = from_matvec(np.eye(3), (4, 2, -1))
aff = nitl.Affine(mat1, reference=ref)
- composed = aff @ mat2
+ composed = aff @ nitl.Affine(mat2)
assert composed.reference is None
- assert composed == nitl.Affine(mat1.dot(mat2))
+ assert composed == nitl.Affine(mat2 @ mat1)
composed = nitl.Affine(mat2) @ aff
assert composed.reference == aff.reference
- assert composed == nitl.Affine(mat2.dot(mat1), reference=ref)
+ assert composed == nitl.Affine(mat1 @ mat2, reference=ref)
diff --git a/nitransforms/tests/test_manip.py b/nitransforms/tests/test_manip.py
index 6dee540e..59f7f3b7 100644
--- a/nitransforms/tests/test_manip.py
+++ b/nitransforms/tests/test_manip.py
@@ -60,6 +60,12 @@ def test_itk_h5(tmp_path, testdata_path):
# A certain tolerance is necessary because of resampling at borders
assert (np.abs(diff) > 1e-3).sum() / diff.size < RMSE_TOL
+ col_moved = xfm.collapse().apply(img_fname, order=0)
+ col_moved.to_filename("nt_collapse_resampled.nii.gz")
+ diff = sw_moved.get_fdata() - col_moved.get_fdata()
+ # A certain tolerance is necessary because of resampling at borders
+ assert (np.abs(diff) > 1e-3).sum() / diff.size < RMSE_TOL
+
@pytest.mark.parametrize("ext0", ["lta", "tfm"])
@pytest.mark.parametrize("ext1", ["lta", "tfm"])
@@ -81,7 +87,7 @@ def test_collapse_affines(tmp_path, data_path, ext0, ext1, ext2):
]
)
assert np.allclose(
- chain.asaffine().matrix,
+ chain.collapse().matrix,
Affine.from_filename(
data_path / "regressions" / f"from-fsnative_to-bold_mode-image.{ext2}",
fmt=f"{FMT[ext2]}",