From d865ec56a5905fd0b3cd1089ce345fe30f1dbcae Mon Sep 17 00:00:00 2001
From: Julien Marabotto <166002186+jmarabotto@users.noreply.github.com>
Date: Fri, 5 Apr 2024 10:00:33 +0200
Subject: [PATCH 01/14] enh: outsource the apply function

---
 nitransforms/base.py       |  95 -------------------------------
 nitransforms/resampling.py | 114 +++++++++++++++++++++++++++++++++++++
 2 files changed, 114 insertions(+), 95 deletions(-)
 create mode 100644 nitransforms/resampling.py

diff --git a/nitransforms/base.py b/nitransforms/base.py
index 68b97f75..3f22990f 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -222,101 +222,6 @@ def ndim(self):
         """Access the dimensions of the reference space."""
         return self.reference.ndim
 
-    def apply(
-        self,
-        spatialimage,
-        reference=None,
-        order=3,
-        mode="constant",
-        cval=0.0,
-        prefilter=True,
-        output_dtype=None,
-    ):
-        """
-        Apply a transformation to an image, resampling on the reference spatial object.
-
-        Parameters
-        ----------
-        spatialimage : `spatialimage`
-            The image object containing the data to be resampled in reference
-            space
-        reference : spatial object, optional
-            The image, surface, or combination thereof containing the coordinates
-            of samples that will be sampled.
-        order : int, optional
-            The order of the spline interpolation, default is 3.
-            The order has to be in the range 0-5.
-        mode : {'constant', 'reflect', 'nearest', 'mirror', 'wrap'}, optional
-            Determines how the input image is extended when the resamplings overflows
-            a border. Default is 'constant'.
-        cval : float, optional
-            Constant value for ``mode='constant'``. Default is 0.0.
-        prefilter: bool, optional
-            Determines if the image's data array is prefiltered with
-            a spline filter before interpolation. The default is ``True``,
-            which will create a temporary *float64* array of filtered values
-            if *order > 1*. If setting this to ``False``, the output will be
-            slightly blurred if *order > 1*, unless the input is prefiltered,
-            i.e. it is the result of calling the spline filter on the original
-            input.
-        output_dtype: dtype specifier, optional
-            The dtype of the returned array or image, if specified.
-            If ``None``, the default behavior is to use the effective dtype of
-            the input image. If slope and/or intercept are defined, the effective
-            dtype is float64, otherwise it is equivalent to the input image's
-            ``get_data_dtype()`` (on-disk type).
-            If ``reference`` is defined, then the return value is an image, with
-            a data array of the effective dtype but with the on-disk dtype set to
-            the input image's on-disk dtype.
-
-        Returns
-        -------
-        resampled : `spatialimage` or ndarray
-            The data imaged after resampling to reference space.
-
-        """
-        if reference is not None and isinstance(reference, (str, Path)):
-            reference = _nbload(str(reference))
-
-        _ref = (
-            self.reference if reference is None else SpatialReference.factory(reference)
-        )
-
-        if _ref is None:
-            raise TransformError("Cannot apply transform without reference")
-
-        if isinstance(spatialimage, (str, Path)):
-            spatialimage = _nbload(str(spatialimage))
-
-        data = np.asanyarray(spatialimage.dataobj)
-        targets = ImageGrid(spatialimage).index(  # data should be an image
-            _as_homogeneous(self.map(_ref.ndcoords.T), dim=_ref.ndim)
-        )
-
-        resampled = ndi.map_coordinates(
-            data,
-            targets.T,
-            output=output_dtype,
-            order=order,
-            mode=mode,
-            cval=cval,
-            prefilter=prefilter,
-        )
-
-        if isinstance(_ref, ImageGrid):  # If reference is grid, reshape
-            hdr = None
-            if _ref.header is not None:
-                hdr = _ref.header.copy()
-                hdr.set_data_dtype(output_dtype or spatialimage.get_data_dtype())
-            moved = spatialimage.__class__(
-                resampled.reshape(_ref.shape),
-                _ref.affine,
-                hdr,
-            )
-            return moved
-
-        return resampled
-
     def map(self, x, inverse=False):
         r"""
         Apply :math:`y = f(x)`.
diff --git a/nitransforms/resampling.py b/nitransforms/resampling.py
new file mode 100644
index 00000000..7d2765ac
--- /dev/null
+++ b/nitransforms/resampling.py
@@ -0,0 +1,114 @@
+# 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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""Resampling utilities."""
+from pathlib import Path
+import numpy as np
+import h5py
+import warnings
+from nibabel.loadsave import load as _nbload
+from nibabel import funcs as _nbfuncs
+from nibabel.nifti1 import intent_codes as INTENT_CODES
+from nibabel.cifti2 import Cifti2Image
+from scipy import ndimage as ndi
+
+
+def apply(
+    transform,
+    spatialimage,
+    reference=None,
+    order=3,
+    mode="constant",
+    cval=0.0,
+    prefilter=True,
+    output_dtype=None,
+):
+    """
+    Apply a transformation to an image, resampling on the reference spatial object.
+
+    Parameters
+    ----------
+    spatialimage : `spatialimage`
+        The image object containing the data to be resampled in reference
+        space
+    reference : spatial object, optional
+        The image, surface, or combination thereof containing the coordinates
+        of samples that will be sampled.
+    order : int, optional
+        The order of the spline interpolation, default is 3.
+        The order has to be in the range 0-5.
+    mode : {'constant', 'reflect', 'nearest', 'mirror', 'wrap'}, optional
+        Determines how the input image is extended when the resamplings overflows
+        a border. Default is 'constant'.
+    cval : float, optional
+        Constant value for ``mode='constant'``. Default is 0.0.
+    prefilter: bool, optional
+        Determines if the image's data array is prefiltered with
+        a spline filter before interpolation. The default is ``True``,
+        which will create a temporary *float64* array of filtered values
+        if *order > 1*. If setting this to ``False``, the output will be
+        slightly blurred if *order > 1*, unless the input is prefiltered,
+        i.e. it is the result of calling the spline filter on the original
+        input.
+    output_dtype: dtype specifier, optional
+        The dtype of the returned array or image, if specified.
+        If ``None``, the default behavior is to use the effective dtype of
+        the input image. If slope and/or intercept are defined, the effective
+        dtype is float64, otherwise it is equivalent to the input image's
+        ``get_data_dtype()`` (on-disk type).
+        If ``reference`` is defined, then the return value is an image, with
+        a data array of the effective dtype but with the on-disk dtype set to
+        the input image's on-disk dtype.
+
+    Returns
+    -------
+    resampled : `spatialimage` or ndarray
+        The data imaged after resampling to reference space.
+
+    """
+    if reference is not None and isinstance(reference, (str, Path)):
+        reference = _nbload(str(reference))
+
+    _ref = (
+        transform.reference if reference is None else SpatialReference.factory(reference)
+    )
+
+    if _ref is None:
+        raise TransformError("Cannot apply transform without reference")
+
+    if isinstance(spatialimage, (str, Path)):
+        spatialimage = _nbload(str(spatialimage))
+
+    data = np.asanyarray(spatialimage.dataobj)
+    targets = ImageGrid(spatialimage).index(  # data should be an image
+        _as_homogeneous(transform.map(_ref.ndcoords.T), dim=_ref.ndim)
+    )
+
+    resampled = ndi.map_coordinates(
+        data,
+        targets.T,
+        output=output_dtype,
+        order=order,
+        mode=mode,
+        cval=cval,
+        prefilter=prefilter,
+    )
+
+    if isinstance(_ref, ImageGrid):  # If reference is grid, reshape
+        hdr = None
+        if _ref.header is not None:
+            hdr = _ref.header.copy()
+            hdr.set_data_dtype(output_dtype or spatialimage.get_data_dtype())
+        moved = spatialimage.__class__(
+            resampled.reshape(_ref.shape),
+            _ref.affine,
+            hdr,
+        )
+        return moved
+
+    return resampled

From d6dca85e0e01e0c1046dc7f15f7f45c6ac66e591 Mon Sep 17 00:00:00 2001
From: Julien Marabotto <166002186+jmarabotto@users.noreply.github.com>
Date: Fri, 5 Apr 2024 10:06:05 +0200
Subject: [PATCH 02/14] sty: pacify flake8

---
 nitransforms/resampling.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/nitransforms/resampling.py b/nitransforms/resampling.py
index 7d2765ac..a876bb12 100644
--- a/nitransforms/resampling.py
+++ b/nitransforms/resampling.py
@@ -9,14 +9,14 @@
 """Resampling utilities."""
 from pathlib import Path
 import numpy as np
-import h5py
-import warnings
 from nibabel.loadsave import load as _nbload
-from nibabel import funcs as _nbfuncs
-from nibabel.nifti1 import intent_codes as INTENT_CODES
-from nibabel.cifti2 import Cifti2Image
-from scipy import ndimage as ndi
 
+from nitransforms.base import (
+    ImageGrid,
+    TransformError,
+    SpatialReference,
+    _as_homogeneous,
+)
 
 def apply(
     transform,

From e299dc182087c37bf70ae1c0044b4e1285b285dd Mon Sep 17 00:00:00 2001
From: Julien Marabotto <166002186+jmarabotto@users.noreply.github.com>
Date: Fri, 5 Apr 2024 10:09:33 +0200
Subject: [PATCH 03/14] sty: fix imports

---
 nitransforms/base.py       | 1 -
 nitransforms/resampling.py | 2 ++
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/nitransforms/base.py b/nitransforms/base.py
index 3f22990f..3d9d6895 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -15,7 +15,6 @@
 from nibabel import funcs as _nbfuncs
 from nibabel.nifti1 import intent_codes as INTENT_CODES
 from nibabel.cifti2 import Cifti2Image
-from scipy import ndimage as ndi
 
 EQUALITY_TOL = 1e-5
 
diff --git a/nitransforms/resampling.py b/nitransforms/resampling.py
index a876bb12..e89b081a 100644
--- a/nitransforms/resampling.py
+++ b/nitransforms/resampling.py
@@ -10,6 +10,7 @@
 from pathlib import Path
 import numpy as np
 from nibabel.loadsave import load as _nbload
+from scipy import ndimage as ndi
 
 from nitransforms.base import (
     ImageGrid,
@@ -18,6 +19,7 @@
     _as_homogeneous,
 )
 
+
 def apply(
     transform,
     spatialimage,

From ffd8a6d404e23008725bf9e162ec4549bf12d465 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 5 Apr 2024 10:35:24 +0200
Subject: [PATCH 04/14] fix: update many apply() calls

---
 nitransforms/cli.py               |  4 ++-
 nitransforms/tests/test_base.py   |  7 +++---
 nitransforms/tests/test_io.py     | 41 ++++++++++++++++++++-----------
 nitransforms/tests/test_linear.py | 16 ++++++------
 4 files changed, 43 insertions(+), 25 deletions(-)

diff --git a/nitransforms/cli.py b/nitransforms/cli.py
index 63b8bed4..8f8f5ce0 100644
--- a/nitransforms/cli.py
+++ b/nitransforms/cli.py
@@ -5,6 +5,7 @@
 
 from .linear import load as linload
 from .nonlinear import load as nlinload
+from .resampling import apply
 
 
 def cli_apply(pargs):
@@ -38,7 +39,8 @@ def cli_apply(pargs):
     # ensure a reference is set
     xfm.reference = pargs.ref or pargs.moving
 
-    moved = xfm.apply(
+    moved = apply(
+        xfm,
         pargs.moving,
         order=pargs.order,
         mode=pargs.mode,
diff --git a/nitransforms/tests/test_base.py b/nitransforms/tests/test_base.py
index 8422ca10..d09096f7 100644
--- a/nitransforms/tests/test_base.py
+++ b/nitransforms/tests/test_base.py
@@ -6,6 +6,7 @@
 
 from ..base import SpatialReference, SampledSpatialData, ImageGrid, TransformBase
 from .. import linear as nitl
+from ..resampling import apply
 
 
 def test_SpatialReference(testdata_path):
@@ -95,7 +96,7 @@ def _to_hdf5(klass, x5_root):
     xfm = TransformBase()
     xfm.reference = fname
     assert xfm.ndim == 3
-    moved = xfm.apply(fname, order=0)
+    moved = apply(xfm, fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
     )
@@ -104,7 +105,7 @@ def _to_hdf5(klass, x5_root):
     xfm = TransformBase()
     xfm.reference = fname
     assert xfm.ndim == 3
-    moved = xfm.apply(str(fname), reference=fname, order=0)
+    moved = apply(xfm, str(fname), reference=fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
     )
@@ -118,7 +119,7 @@ def _to_hdf5(klass, x5_root):
             )
         ]
     )
-    giimoved = xfm.apply(fname, reference=gii, order=0)
+    giimoved = apply(xfm, fname, reference=gii, order=0)
     assert np.allclose(giimoved.reshape(xfm.reference.shape), moved.get_fdata())
 
     # Test to_filename
diff --git a/nitransforms/tests/test_io.py b/nitransforms/tests/test_io.py
index bcee9198..0cc79d15 100644
--- a/nitransforms/tests/test_io.py
+++ b/nitransforms/tests/test_io.py
@@ -28,6 +28,8 @@
 )
 from nitransforms.io.base import LinearParameters, TransformIOError, TransformFileError
 from nitransforms.conftest import _datadir, _testdir
+from nitransforms.resampling import apply
+
 
 LPS = np.diag([-1, -1, 1, 1])
 ITK_MAT = LPS.dot(np.ones((4, 4)).dot(LPS))
@@ -497,10 +499,13 @@ def test_afni_oblique(tmpdir, parameters, swapaxes, testdata_path, dir_x, dir_y,
     assert np.allclose(card_aff, nb.load("deob_3drefit.nii.gz").affine)
 
     # Check that nitransforms can emulate 3drefit -deoblique
-    nt3drefit = Affine(
-        afni._cardinal_rotation(img.affine, False),
-        reference="deob_3drefit.nii.gz",
-    ).apply("orig.nii.gz")
+    nt3drefit = apply(
+        Affine(
+            afni._cardinal_rotation(img.affine, False),
+            reference="deob_3drefit.nii.gz",
+        ),
+        "orig.nii.gz",
+    )
 
     diff = (
         np.asanyarray(img.dataobj, dtype="uint8")
@@ -509,10 +514,13 @@ def test_afni_oblique(tmpdir, parameters, swapaxes, testdata_path, dir_x, dir_y,
     assert np.sqrt((diff[10:-10, 10:-10, 10:-10] ** 2).mean()) < 0.1
 
     # Check that nitransforms can revert 3drefit -deoblique
-    nt_undo3drefit = Affine(
-        afni._cardinal_rotation(img.affine, True),
-        reference="orig.nii.gz",
-    ).apply("deob_3drefit.nii.gz")
+    nt_undo3drefit = apply(
+        Affine(
+            afni._cardinal_rotation(img.affine, True),
+            reference="orig.nii.gz",
+        ),
+        "deob_3drefit.nii.gz",
+    )
 
     diff = (
         np.asanyarray(img.dataobj, dtype="uint8")
@@ -531,16 +539,21 @@ def test_afni_oblique(tmpdir, parameters, swapaxes, testdata_path, dir_x, dir_y,
     assert np.allclose(deobaff, deobnii.affine)
 
     # Check resampling in deobliqued grid
-    ntdeobnii = Affine(np.eye(4), reference=deobnii.__class__(
-        np.zeros(deobshape, dtype="uint8"),
-        deobaff,
-        deobnii.header
-    )).apply(img, order=0)
+    ntdeobnii = apply(
+        Affine(np.eye(4), reference=deobnii.__class__(
+            np.zeros(deobshape, dtype="uint8"),
+            deobaff,
+            deobnii.header
+        )),
+        img,
+        order=0,
+    )
 
     # Generate an internal box to exclude border effects
     box = np.zeros(img.shape, dtype="uint8")
     box[10:-10, 10:-10, 10:-10] = 1
-    ntdeobmask = Affine(np.eye(4), reference=ntdeobnii).apply(
+    ntdeobmask = apply(
+        Affine(np.eye(4), reference=ntdeobnii),
         nb.Nifti1Image(box, img.affine, img.header),
         order=0,
     )
diff --git a/nitransforms/tests/test_linear.py b/nitransforms/tests/test_linear.py
index 2957f59c..9a06fe32 100644
--- a/nitransforms/tests/test_linear.py
+++ b/nitransforms/tests/test_linear.py
@@ -13,6 +13,7 @@
 from nibabel.affines import from_matvec
 from nitransforms import linear as nitl
 from nitransforms import io
+from nitransforms.resampling import apply
 from .utils import assert_affines_by_filename
 
 RMSE_TOL = 0.1
@@ -285,7 +286,7 @@ def test_apply_linear_transform(tmpdir, get_testdata, get_testmask, image_orient
     assert exit_code == 0
     sw_moved_mask = nb.load("resampled_brainmask.nii.gz")
 
-    nt_moved_mask = xfm.apply(msk, order=0)
+    nt_moved_mask = apply(xfm, msk, order=0)
     nt_moved_mask.set_data_dtype(msk.get_data_dtype())
     nt_moved_mask.to_filename("ntmask.nii.gz")
     diff = np.asanyarray(sw_moved_mask.dataobj) - np.asanyarray(nt_moved_mask.dataobj)
@@ -305,7 +306,7 @@ def test_apply_linear_transform(tmpdir, get_testdata, get_testmask, image_orient
     sw_moved = nb.load("resampled.nii.gz")
     sw_moved.set_data_dtype(img.get_data_dtype())
 
-    nt_moved = xfm.apply(img, order=0)
+    nt_moved = apply(xfm, img, order=0)
     diff = (
         np.asanyarray(sw_moved.dataobj, dtype=sw_moved.get_data_dtype())
         - np.asanyarray(nt_moved.dataobj, dtype=nt_moved.get_data_dtype())
@@ -314,7 +315,7 @@ def test_apply_linear_transform(tmpdir, get_testdata, get_testmask, image_orient
     # A certain tolerance is necessary because of resampling at borders
     assert np.sqrt((diff[brainmask] ** 2).mean()) < RMSE_TOL
 
-    nt_moved = xfm.apply("img.nii.gz", order=0)
+    nt_moved = apply(xfm, "img.nii.gz", order=0)
     diff = (
         np.asanyarray(sw_moved.dataobj, dtype=sw_moved.get_data_dtype())
         - np.asanyarray(nt_moved.dataobj, dtype=nt_moved.get_data_dtype())
@@ -343,8 +344,8 @@ def test_LinearTransformsMapping_apply(tmp_path, data_path, testdata_path):
     assert isinstance(hmc, nitl.LinearTransformsMapping)
 
     # Test-case: realign functional data on to sbref
-    nii = hmc.apply(
-        testdata_path / "func.nii.gz", order=1, reference=testdata_path / "sbref.nii.gz"
+    nii = apply(
+        hmc, testdata_path / "func.nii.gz", order=1, reference=testdata_path / "sbref.nii.gz"
     )
     assert nii.dataobj.shape[-1] == len(hmc)
 
@@ -352,13 +353,14 @@ def test_LinearTransformsMapping_apply(tmp_path, data_path, testdata_path):
     hmcinv = nitl.LinearTransformsMapping(
         np.linalg.inv(hmc.matrix), reference=testdata_path / "func.nii.gz"
     )
-    nii = hmcinv.apply(testdata_path / "fmap.nii.gz", order=1)
+    nii = apply(hmcinv, testdata_path / "fmap.nii.gz", order=1)
     assert nii.dataobj.shape[-1] == len(hmc)
 
     # Ensure a ValueError is issued when trying to do weird stuff
     hmc = nitl.LinearTransformsMapping(hmc.matrix[:1, ...])
     with pytest.raises(ValueError):
-        hmc.apply(
+        apply(
+            hmc,
             testdata_path / "func.nii.gz",
             order=1,
             reference=testdata_path / "sbref.nii.gz",

From 150c14579c66ddb776dc8cacf718ddffb9c117cd Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 10:43:53 +0200
Subject: [PATCH 05/14] Implement ndim

Tranformbase -> now raises TypeError; Affine -> overshadows TransformBase's property and returns self._matrix.ndim + 1. To be applied to LinearTransformMapping (Currently TypeError)
---
 commandline_for_tests.txt       |   7 +++++++
 nitransforms/.DS_Store          | Bin 0 -> 6148 bytes
 nitransforms/base.py            |  16 ++++++++++++++--
 nitransforms/io/.DS_Store       | Bin 0 -> 6148 bytes
 nitransforms/linear.py          |   9 +++++++--
 nitransforms/tests/test_base.py |  11 +++++++++--
 6 files changed, 37 insertions(+), 6 deletions(-)
 create mode 100644 commandline_for_tests.txt
 create mode 100644 nitransforms/.DS_Store
 create mode 100644 nitransforms/io/.DS_Store

diff --git a/commandline_for_tests.txt b/commandline_for_tests.txt
new file mode 100644
index 00000000..87c85ea2
--- /dev/null
+++ b/commandline_for_tests.txt
@@ -0,0 +1,7 @@
+Terminal command line to test code:
+
+>>> TEST_DATA_HOME=$HOME/Desktop/nitransforms-tests python3 -m pytest
+
+Also works for a path to a specific test, eg:
+
+>>> TEST_DATA_HOME=$HOME/Desktop/nitransforms-tests python3 -m pytest ~/workspace/nitransforms/nitransforms/tests/test_base.py::test_TransformBase 
\ No newline at end of file
diff --git a/nitransforms/.DS_Store b/nitransforms/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
GIT binary patch
literal 6148
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zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
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j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

literal 0
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diff --git a/nitransforms/base.py b/nitransforms/base.py
index 3d9d6895..42119d9c 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -15,6 +15,7 @@
 from nibabel import funcs as _nbfuncs
 from nibabel.nifti1 import intent_codes as INTENT_CODES
 from nibabel.cifti2 import Cifti2Image
+from nitransforms import linear as nitl
 
 EQUALITY_TOL = 1e-5
 
@@ -177,7 +178,8 @@ def __ne__(self, other):
 class TransformBase:
     """Abstract image class to represent transforms."""
 
-    __slots__ = ("_reference",)
+    __slots__ = ("_reference", "_ndim",)
+
 
     def __init__(self, reference=None):
         """Instantiate a transform."""
@@ -211,6 +213,13 @@ def reference(self):
         if self._reference is None:
             warnings.warn("Reference space not set")
         return self._reference
+    
+    @property
+    def reference(_ndim):
+        """Access a reference space where data will be resampled onto."""
+        if _ndim._reference is None:
+            warnings.warn("Reference space not set")
+        return _ndim._reference
 
     @reference.setter
     def reference(self, image):
@@ -219,7 +228,8 @@ def reference(self, image):
     @property
     def ndim(self):
         """Access the dimensions of the reference space."""
-        return self.reference.ndim
+        #return self.reference.ndim
+        raise TypeError("TransformBase has no dimensions")
 
     def map(self, x, inverse=False):
         r"""
@@ -287,3 +297,5 @@ def _as_homogeneous(xyz, dtype="float32", dim=3):
 def _apply_affine(x, affine, dim):
     """Get the image array's indexes corresponding to coordinates."""
     return affine.dot(_as_homogeneous(x, dim=dim).T)[:dim, ...].T
+
+#import pdb; pdb.set_trace()
diff --git a/nitransforms/io/.DS_Store b/nitransforms/io/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..db6d5fb599944be892b217b8202a87b66720ca2f
GIT binary patch
literal 6148
zcmeHKJBk895Uo-J!Nkz8uiy<D(Gz%pQCwMr#T8)%vxz*HNAuN(g<&+<U=w)-Rj<3c
zUJvtvsVNcB#m~oFWGW(KxS`xE^v%xAdp5|70^zu0CtLVI_R{pKpC^nvL3JZ1xpw%?
zWqm$=eIGyL_UCkFsQ?wA0#twsP=P-xV7(VMo&+*d0V+TReig9qLxCIC#5T}B9SA-G
z07po>VePX7uvh|E6Wc&!U>a0lP&G#k4Lb5A>uO>f7<ADbJ~W@KIiaXO9rqV67p;Me
zRDcR}6&S{LYW;r&e=+}eN!(EZD)3ec=xDiKF7Qg(TYE2Oy|%zNaI3k)&9HU~g12L!
iw_|Lq9nZWd>WZy#UK86urz7ulAb$o-7aA4#Zv`F!AQhhg

literal 0
HcmV?d00001

diff --git a/nitransforms/linear.py b/nitransforms/linear.py
index eb4a95d7..569ac9c2 100644
--- a/nitransforms/linear.py
+++ b/nitransforms/linear.py
@@ -143,6 +143,11 @@ def matrix(self):
         """Access the internal representation of this affine."""
         return self._matrix
 
+    @property
+    def ndim(self):
+        """Access the internal representation of this affine."""
+        return self._matrix.ndim + 1
+    
     def map(self, x, inverse=False):
         r"""
         Apply :math:`y = f(x)`.
@@ -270,7 +275,7 @@ def __repr__(self):
 
         """
         return repr(self.matrix)
-
+    
 
 class LinearTransformsMapping(Affine):
     """Represents a series of linear transforms."""
@@ -533,4 +538,4 @@ def load(filename, fmt=None, reference=None, moving=None):
     if isinstance(xfm, LinearTransformsMapping) and len(xfm) == 1:
         xfm = xfm[0]
 
-    return xfm
+    return xfm
\ No newline at end of file
diff --git a/nitransforms/tests/test_base.py b/nitransforms/tests/test_base.py
index d09096f7..893fe80c 100644
--- a/nitransforms/tests/test_base.py
+++ b/nitransforms/tests/test_base.py
@@ -95,7 +95,8 @@ def _to_hdf5(klass, x5_root):
     # Test identity transform
     xfm = TransformBase()
     xfm.reference = fname
-    assert xfm.ndim == 3
+    with pytest.raises(TypeError):
+        _ = xfm.ndim
     moved = apply(xfm, fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
@@ -104,12 +105,18 @@ def _to_hdf5(klass, x5_root):
     # Test identity transform - setting reference
     xfm = TransformBase()
     xfm.reference = fname
-    assert xfm.ndim == 3
+    with pytest.raises(TypeError):
+        _ = xfm.ndim
     moved = apply(xfm, str(fname), reference=fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
     )
 
+    #Test ndim returned by affine
+    #breakpoint()
+    assert nitl.Affine().ndim == 3
+    assert nitl.LinearTransformsMapping(xfm.matrix).ndim == 4
+
     # Test applying to Gifti
     gii = nb.gifti.GiftiImage(
         darrays=[

From f3529ced803ed1fef95034629d8de9c295f171db Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 15:57:33 +0200
Subject: [PATCH 06/14] ENH: Implement_ndim

Added two tests for ndim: assert nitl.Affine().ndim == 3; assert nitl.LinearTransformsMapping([nitl.Affine()]).ndim == 4 .
---
 nitransforms/tests/test_base.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nitransforms/tests/test_base.py b/nitransforms/tests/test_base.py
index 893fe80c..97c452c6 100644
--- a/nitransforms/tests/test_base.py
+++ b/nitransforms/tests/test_base.py
@@ -113,9 +113,8 @@ def _to_hdf5(klass, x5_root):
     )
 
     #Test ndim returned by affine
-    #breakpoint()
     assert nitl.Affine().ndim == 3
-    assert nitl.LinearTransformsMapping(xfm.matrix).ndim == 4
+    assert nitl.LinearTransformsMapping([nitl.Affine()]).ndim == 4
 
     # Test applying to Gifti
     gii = nb.gifti.GiftiImage(

From 3d40b93d1f2bc9ac85d25475189b95fb8704ac7a Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 16:44:33 +0200
Subject: [PATCH 07/14] enh: add a test on ndim

---
 nitransforms/base.py            | 1 -
 nitransforms/tests/test_base.py | 4 +++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/nitransforms/base.py b/nitransforms/base.py
index 42119d9c..05f72d7a 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -15,7 +15,6 @@
 from nibabel import funcs as _nbfuncs
 from nibabel.nifti1 import intent_codes as INTENT_CODES
 from nibabel.cifti2 import Cifti2Image
-from nitransforms import linear as nitl
 
 EQUALITY_TOL = 1e-5
 
diff --git a/nitransforms/tests/test_base.py b/nitransforms/tests/test_base.py
index 97c452c6..5b50e656 100644
--- a/nitransforms/tests/test_base.py
+++ b/nitransforms/tests/test_base.py
@@ -114,7 +114,9 @@ def _to_hdf5(klass, x5_root):
 
     #Test ndim returned by affine
     assert nitl.Affine().ndim == 3
-    assert nitl.LinearTransformsMapping([nitl.Affine()]).ndim == 4
+    assert nitl.LinearTransformsMapping(
+        [nitl.Affine(), nitl.Affine()]
+    ).ndim == 4
 
     # Test applying to Gifti
     gii = nb.gifti.GiftiImage(

From abe016ef9b6c9c30a51692a5da6a17ae89b5aba7 Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 16:55:30 +0200
Subject: [PATCH 08/14] fix: remove straneous files, revert changes from other
 branch

---
 commandline_for_tests.txt  |   7 ---
 nitransforms/.DS_Store     | Bin 6148 -> 0 bytes
 nitransforms/base.py       |  92 +++++++++++++++++++++++++++++
 nitransforms/resampling.py | 116 -------------------------------------
 4 files changed, 92 insertions(+), 123 deletions(-)
 delete mode 100644 commandline_for_tests.txt
 delete mode 100644 nitransforms/.DS_Store
 delete mode 100644 nitransforms/resampling.py

diff --git a/commandline_for_tests.txt b/commandline_for_tests.txt
deleted file mode 100644
index 87c85ea2..00000000
--- a/commandline_for_tests.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-Terminal command line to test code:
-
->>> TEST_DATA_HOME=$HOME/Desktop/nitransforms-tests python3 -m pytest
-
-Also works for a path to a specific test, eg:
-
->>> TEST_DATA_HOME=$HOME/Desktop/nitransforms-tests python3 -m pytest ~/workspace/nitransforms/nitransforms/tests/test_base.py::test_TransformBase 
\ No newline at end of file
diff --git a/nitransforms/.DS_Store b/nitransforms/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

diff --git a/nitransforms/base.py b/nitransforms/base.py
index 05f72d7a..66b3808f 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -230,6 +230,98 @@ def ndim(self):
         #return self.reference.ndim
         raise TypeError("TransformBase has no dimensions")
 
+    def apply(
+        self,
+        spatialimage,
+        reference=None,
+        order=3,
+        mode="constant",
+        cval=0.0,
+        prefilter=True,
+        output_dtype=None,
+    ):
+        """
+        Apply a transformation to an image, resampling on the reference spatial object.
+        Parameters
+        ----------
+        spatialimage : `spatialimage`
+            The image object containing the data to be resampled in reference
+            space
+        reference : spatial object, optional
+            The image, surface, or combination thereof containing the coordinates
+            of samples that will be sampled.
+        order : int, optional
+            The order of the spline interpolation, default is 3.
+            The order has to be in the range 0-5.
+        mode : {'constant', 'reflect', 'nearest', 'mirror', 'wrap'}, optional
+            Determines how the input image is extended when the resamplings overflows
+            a border. Default is 'constant'.
+        cval : float, optional
+            Constant value for ``mode='constant'``. Default is 0.0.
+        prefilter: bool, optional
+            Determines if the image's data array is prefiltered with
+            a spline filter before interpolation. The default is ``True``,
+            which will create a temporary *float64* array of filtered values
+            if *order > 1*. If setting this to ``False``, the output will be
+            slightly blurred if *order > 1*, unless the input is prefiltered,
+            i.e. it is the result of calling the spline filter on the original
+            input.
+        output_dtype: dtype specifier, optional
+            The dtype of the returned array or image, if specified.
+            If ``None``, the default behavior is to use the effective dtype of
+            the input image. If slope and/or intercept are defined, the effective
+            dtype is float64, otherwise it is equivalent to the input image's
+            ``get_data_dtype()`` (on-disk type).
+            If ``reference`` is defined, then the return value is an image, with
+            a data array of the effective dtype but with the on-disk dtype set to
+            the input image's on-disk dtype.
+        Returns
+        -------
+        resampled : `spatialimage` or ndarray
+            The data imaged after resampling to reference space.
+        """
+        if reference is not None and isinstance(reference, (str, Path)):
+            reference = _nbload(str(reference))
+
+        _ref = (
+            self.reference if reference is None else SpatialReference.factory(reference)
+        )
+
+        if _ref is None:
+            raise TransformError("Cannot apply transform without reference")
+
+        if isinstance(spatialimage, (str, Path)):
+            spatialimage = _nbload(str(spatialimage))
+
+        data = np.asanyarray(spatialimage.dataobj)
+        targets = ImageGrid(spatialimage).index(  # data should be an image
+            _as_homogeneous(self.map(_ref.ndcoords.T), dim=_ref.ndim)
+        )
+
+        resampled = ndi.map_coordinates(
+            data,
+            targets.T,
+            output=output_dtype,
+            order=order,
+            mode=mode,
+            cval=cval,
+            prefilter=prefilter,
+        )
+
+        if isinstance(_ref, ImageGrid):  # If reference is grid, reshape
+            hdr = None
+            if _ref.header is not None:
+                hdr = _ref.header.copy()
+                hdr.set_data_dtype(output_dtype or spatialimage.get_data_dtype())
+            moved = spatialimage.__class__(
+                resampled.reshape(_ref.shape),
+                _ref.affine,
+                hdr,
+            )
+            return moved
+
+        return resampled
+
     def map(self, x, inverse=False):
         r"""
         Apply :math:`y = f(x)`.
diff --git a/nitransforms/resampling.py b/nitransforms/resampling.py
deleted file mode 100644
index e89b081a..00000000
--- a/nitransforms/resampling.py
+++ /dev/null
@@ -1,116 +0,0 @@
-# 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.
-#
-### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Resampling utilities."""
-from pathlib import Path
-import numpy as np
-from nibabel.loadsave import load as _nbload
-from scipy import ndimage as ndi
-
-from nitransforms.base import (
-    ImageGrid,
-    TransformError,
-    SpatialReference,
-    _as_homogeneous,
-)
-
-
-def apply(
-    transform,
-    spatialimage,
-    reference=None,
-    order=3,
-    mode="constant",
-    cval=0.0,
-    prefilter=True,
-    output_dtype=None,
-):
-    """
-    Apply a transformation to an image, resampling on the reference spatial object.
-
-    Parameters
-    ----------
-    spatialimage : `spatialimage`
-        The image object containing the data to be resampled in reference
-        space
-    reference : spatial object, optional
-        The image, surface, or combination thereof containing the coordinates
-        of samples that will be sampled.
-    order : int, optional
-        The order of the spline interpolation, default is 3.
-        The order has to be in the range 0-5.
-    mode : {'constant', 'reflect', 'nearest', 'mirror', 'wrap'}, optional
-        Determines how the input image is extended when the resamplings overflows
-        a border. Default is 'constant'.
-    cval : float, optional
-        Constant value for ``mode='constant'``. Default is 0.0.
-    prefilter: bool, optional
-        Determines if the image's data array is prefiltered with
-        a spline filter before interpolation. The default is ``True``,
-        which will create a temporary *float64* array of filtered values
-        if *order > 1*. If setting this to ``False``, the output will be
-        slightly blurred if *order > 1*, unless the input is prefiltered,
-        i.e. it is the result of calling the spline filter on the original
-        input.
-    output_dtype: dtype specifier, optional
-        The dtype of the returned array or image, if specified.
-        If ``None``, the default behavior is to use the effective dtype of
-        the input image. If slope and/or intercept are defined, the effective
-        dtype is float64, otherwise it is equivalent to the input image's
-        ``get_data_dtype()`` (on-disk type).
-        If ``reference`` is defined, then the return value is an image, with
-        a data array of the effective dtype but with the on-disk dtype set to
-        the input image's on-disk dtype.
-
-    Returns
-    -------
-    resampled : `spatialimage` or ndarray
-        The data imaged after resampling to reference space.
-
-    """
-    if reference is not None and isinstance(reference, (str, Path)):
-        reference = _nbload(str(reference))
-
-    _ref = (
-        transform.reference if reference is None else SpatialReference.factory(reference)
-    )
-
-    if _ref is None:
-        raise TransformError("Cannot apply transform without reference")
-
-    if isinstance(spatialimage, (str, Path)):
-        spatialimage = _nbload(str(spatialimage))
-
-    data = np.asanyarray(spatialimage.dataobj)
-    targets = ImageGrid(spatialimage).index(  # data should be an image
-        _as_homogeneous(transform.map(_ref.ndcoords.T), dim=_ref.ndim)
-    )
-
-    resampled = ndi.map_coordinates(
-        data,
-        targets.T,
-        output=output_dtype,
-        order=order,
-        mode=mode,
-        cval=cval,
-        prefilter=prefilter,
-    )
-
-    if isinstance(_ref, ImageGrid):  # If reference is grid, reshape
-        hdr = None
-        if _ref.header is not None:
-            hdr = _ref.header.copy()
-            hdr.set_data_dtype(output_dtype or spatialimage.get_data_dtype())
-        moved = spatialimage.__class__(
-            resampled.reshape(_ref.shape),
-            _ref.affine,
-            hdr,
-        )
-        return moved
-
-    return resampled

From 180ec18fdb0d8a2c1a18e6777d3807530130a78a Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 16:59:39 +0200
Subject: [PATCH 09/14] enh: revert unrelated changes

---
 nitransforms/tests/test_base.py   |  7 +++---
 nitransforms/tests/test_io.py     | 41 +++++++++++--------------------
 nitransforms/tests/test_linear.py | 16 ++++++------
 3 files changed, 24 insertions(+), 40 deletions(-)

diff --git a/nitransforms/tests/test_base.py b/nitransforms/tests/test_base.py
index 5b50e656..f315cc6c 100644
--- a/nitransforms/tests/test_base.py
+++ b/nitransforms/tests/test_base.py
@@ -6,7 +6,6 @@
 
 from ..base import SpatialReference, SampledSpatialData, ImageGrid, TransformBase
 from .. import linear as nitl
-from ..resampling import apply
 
 
 def test_SpatialReference(testdata_path):
@@ -97,7 +96,7 @@ def _to_hdf5(klass, x5_root):
     xfm.reference = fname
     with pytest.raises(TypeError):
         _ = xfm.ndim
-    moved = apply(xfm, fname, order=0)
+    moved = xfm.apply(fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
     )
@@ -107,7 +106,7 @@ def _to_hdf5(klass, x5_root):
     xfm.reference = fname
     with pytest.raises(TypeError):
         _ = xfm.ndim
-    moved = apply(xfm, str(fname), reference=fname, order=0)
+    moved = xfm.apply(str(fname), reference=fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
     )
@@ -127,7 +126,7 @@ def _to_hdf5(klass, x5_root):
             )
         ]
     )
-    giimoved = apply(xfm, fname, reference=gii, order=0)
+    giimoved = xfm.apply(fname, reference=gii, order=0)
     assert np.allclose(giimoved.reshape(xfm.reference.shape), moved.get_fdata())
 
     # Test to_filename
diff --git a/nitransforms/tests/test_io.py b/nitransforms/tests/test_io.py
index 0cc79d15..bcee9198 100644
--- a/nitransforms/tests/test_io.py
+++ b/nitransforms/tests/test_io.py
@@ -28,8 +28,6 @@
 )
 from nitransforms.io.base import LinearParameters, TransformIOError, TransformFileError
 from nitransforms.conftest import _datadir, _testdir
-from nitransforms.resampling import apply
-
 
 LPS = np.diag([-1, -1, 1, 1])
 ITK_MAT = LPS.dot(np.ones((4, 4)).dot(LPS))
@@ -499,13 +497,10 @@ def test_afni_oblique(tmpdir, parameters, swapaxes, testdata_path, dir_x, dir_y,
     assert np.allclose(card_aff, nb.load("deob_3drefit.nii.gz").affine)
 
     # Check that nitransforms can emulate 3drefit -deoblique
-    nt3drefit = apply(
-        Affine(
-            afni._cardinal_rotation(img.affine, False),
-            reference="deob_3drefit.nii.gz",
-        ),
-        "orig.nii.gz",
-    )
+    nt3drefit = Affine(
+        afni._cardinal_rotation(img.affine, False),
+        reference="deob_3drefit.nii.gz",
+    ).apply("orig.nii.gz")
 
     diff = (
         np.asanyarray(img.dataobj, dtype="uint8")
@@ -514,13 +509,10 @@ def test_afni_oblique(tmpdir, parameters, swapaxes, testdata_path, dir_x, dir_y,
     assert np.sqrt((diff[10:-10, 10:-10, 10:-10] ** 2).mean()) < 0.1
 
     # Check that nitransforms can revert 3drefit -deoblique
-    nt_undo3drefit = apply(
-        Affine(
-            afni._cardinal_rotation(img.affine, True),
-            reference="orig.nii.gz",
-        ),
-        "deob_3drefit.nii.gz",
-    )
+    nt_undo3drefit = Affine(
+        afni._cardinal_rotation(img.affine, True),
+        reference="orig.nii.gz",
+    ).apply("deob_3drefit.nii.gz")
 
     diff = (
         np.asanyarray(img.dataobj, dtype="uint8")
@@ -539,21 +531,16 @@ def test_afni_oblique(tmpdir, parameters, swapaxes, testdata_path, dir_x, dir_y,
     assert np.allclose(deobaff, deobnii.affine)
 
     # Check resampling in deobliqued grid
-    ntdeobnii = apply(
-        Affine(np.eye(4), reference=deobnii.__class__(
-            np.zeros(deobshape, dtype="uint8"),
-            deobaff,
-            deobnii.header
-        )),
-        img,
-        order=0,
-    )
+    ntdeobnii = Affine(np.eye(4), reference=deobnii.__class__(
+        np.zeros(deobshape, dtype="uint8"),
+        deobaff,
+        deobnii.header
+    )).apply(img, order=0)
 
     # Generate an internal box to exclude border effects
     box = np.zeros(img.shape, dtype="uint8")
     box[10:-10, 10:-10, 10:-10] = 1
-    ntdeobmask = apply(
-        Affine(np.eye(4), reference=ntdeobnii),
+    ntdeobmask = Affine(np.eye(4), reference=ntdeobnii).apply(
         nb.Nifti1Image(box, img.affine, img.header),
         order=0,
     )
diff --git a/nitransforms/tests/test_linear.py b/nitransforms/tests/test_linear.py
index 9a06fe32..2957f59c 100644
--- a/nitransforms/tests/test_linear.py
+++ b/nitransforms/tests/test_linear.py
@@ -13,7 +13,6 @@
 from nibabel.affines import from_matvec
 from nitransforms import linear as nitl
 from nitransforms import io
-from nitransforms.resampling import apply
 from .utils import assert_affines_by_filename
 
 RMSE_TOL = 0.1
@@ -286,7 +285,7 @@ def test_apply_linear_transform(tmpdir, get_testdata, get_testmask, image_orient
     assert exit_code == 0
     sw_moved_mask = nb.load("resampled_brainmask.nii.gz")
 
-    nt_moved_mask = apply(xfm, msk, order=0)
+    nt_moved_mask = xfm.apply(msk, order=0)
     nt_moved_mask.set_data_dtype(msk.get_data_dtype())
     nt_moved_mask.to_filename("ntmask.nii.gz")
     diff = np.asanyarray(sw_moved_mask.dataobj) - np.asanyarray(nt_moved_mask.dataobj)
@@ -306,7 +305,7 @@ def test_apply_linear_transform(tmpdir, get_testdata, get_testmask, image_orient
     sw_moved = nb.load("resampled.nii.gz")
     sw_moved.set_data_dtype(img.get_data_dtype())
 
-    nt_moved = apply(xfm, img, order=0)
+    nt_moved = xfm.apply(img, order=0)
     diff = (
         np.asanyarray(sw_moved.dataobj, dtype=sw_moved.get_data_dtype())
         - np.asanyarray(nt_moved.dataobj, dtype=nt_moved.get_data_dtype())
@@ -315,7 +314,7 @@ def test_apply_linear_transform(tmpdir, get_testdata, get_testmask, image_orient
     # A certain tolerance is necessary because of resampling at borders
     assert np.sqrt((diff[brainmask] ** 2).mean()) < RMSE_TOL
 
-    nt_moved = apply(xfm, "img.nii.gz", order=0)
+    nt_moved = xfm.apply("img.nii.gz", order=0)
     diff = (
         np.asanyarray(sw_moved.dataobj, dtype=sw_moved.get_data_dtype())
         - np.asanyarray(nt_moved.dataobj, dtype=nt_moved.get_data_dtype())
@@ -344,8 +343,8 @@ def test_LinearTransformsMapping_apply(tmp_path, data_path, testdata_path):
     assert isinstance(hmc, nitl.LinearTransformsMapping)
 
     # Test-case: realign functional data on to sbref
-    nii = apply(
-        hmc, testdata_path / "func.nii.gz", order=1, reference=testdata_path / "sbref.nii.gz"
+    nii = hmc.apply(
+        testdata_path / "func.nii.gz", order=1, reference=testdata_path / "sbref.nii.gz"
     )
     assert nii.dataobj.shape[-1] == len(hmc)
 
@@ -353,14 +352,13 @@ def test_LinearTransformsMapping_apply(tmp_path, data_path, testdata_path):
     hmcinv = nitl.LinearTransformsMapping(
         np.linalg.inv(hmc.matrix), reference=testdata_path / "func.nii.gz"
     )
-    nii = apply(hmcinv, testdata_path / "fmap.nii.gz", order=1)
+    nii = hmcinv.apply(testdata_path / "fmap.nii.gz", order=1)
     assert nii.dataobj.shape[-1] == len(hmc)
 
     # Ensure a ValueError is issued when trying to do weird stuff
     hmc = nitl.LinearTransformsMapping(hmc.matrix[:1, ...])
     with pytest.raises(ValueError):
-        apply(
-            hmc,
+        hmc.apply(
             testdata_path / "func.nii.gz",
             order=1,
             reference=testdata_path / "sbref.nii.gz",

From c0e2a98fe3459243ecb3ac6aaba18fd91c209b42 Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 17:00:55 +0200
Subject: [PATCH 10/14] enh: revert unrelated changes

---
 nitransforms/cli.py       |   4 +---
 nitransforms/io/.DS_Store | Bin 6148 -> 0 bytes
 2 files changed, 1 insertion(+), 3 deletions(-)
 delete mode 100644 nitransforms/io/.DS_Store

diff --git a/nitransforms/cli.py b/nitransforms/cli.py
index 8f8f5ce0..63b8bed4 100644
--- a/nitransforms/cli.py
+++ b/nitransforms/cli.py
@@ -5,7 +5,6 @@
 
 from .linear import load as linload
 from .nonlinear import load as nlinload
-from .resampling import apply
 
 
 def cli_apply(pargs):
@@ -39,8 +38,7 @@ def cli_apply(pargs):
     # ensure a reference is set
     xfm.reference = pargs.ref or pargs.moving
 
-    moved = apply(
-        xfm,
+    moved = xfm.apply(
         pargs.moving,
         order=pargs.order,
         mode=pargs.mode,
diff --git a/nitransforms/io/.DS_Store b/nitransforms/io/.DS_Store
deleted file mode 100644
index db6d5fb599944be892b217b8202a87b66720ca2f..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeHKJBk895Uo-J!Nkz8uiy<D(Gz%pQCwMr#T8)%vxz*HNAuN(g<&+<U=w)-Rj<3c
zUJvtvsVNcB#m~oFWGW(KxS`xE^v%xAdp5|70^zu0CtLVI_R{pKpC^nvL3JZ1xpw%?
zWqm$=eIGyL_UCkFsQ?wA0#twsP=P-xV7(VMo&+*d0V+TReig9qLxCIC#5T}B9SA-G
z07po>VePX7uvh|E6Wc&!U>a0lP&G#k4Lb5A>uO>f7<ADbJ~W@KIiaXO9rqV67p;Me
zRDcR}6&S{LYW;r&e=+}eN!(EZD)3ec=xDiKF7Qg(TYE2Oy|%zNaI3k)&9HU~g12L!
iw_|Lq9nZWd>WZy#UK86urz7ulAb$o-7aA4#Zv`F!AQhhg


From 90e529ba664e54d52a6fae914dc3b9fc309e2190 Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 17:03:52 +0200
Subject: [PATCH 11/14] enh: revert unrelated changes

---
 nitransforms/base.py | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/nitransforms/base.py b/nitransforms/base.py
index 66b3808f..117d4064 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -15,6 +15,7 @@
 from nibabel import funcs as _nbfuncs
 from nibabel.nifti1 import intent_codes as INTENT_CODES
 from nibabel.cifti2 import Cifti2Image
+from scipy import ndimage as ndi
 
 EQUALITY_TOL = 1e-5
 
@@ -212,13 +213,6 @@ def reference(self):
         if self._reference is None:
             warnings.warn("Reference space not set")
         return self._reference
-    
-    @property
-    def reference(_ndim):
-        """Access a reference space where data will be resampled onto."""
-        if _ndim._reference is None:
-            warnings.warn("Reference space not set")
-        return _ndim._reference
 
     @reference.setter
     def reference(self, image):
@@ -227,7 +221,6 @@ def reference(self, image):
     @property
     def ndim(self):
         """Access the dimensions of the reference space."""
-        #return self.reference.ndim
         raise TypeError("TransformBase has no dimensions")
 
     def apply(
@@ -242,6 +235,7 @@ def apply(
     ):
         """
         Apply a transformation to an image, resampling on the reference spatial object.
+
         Parameters
         ----------
         spatialimage : `spatialimage`
@@ -275,10 +269,12 @@ def apply(
             If ``reference`` is defined, then the return value is an image, with
             a data array of the effective dtype but with the on-disk dtype set to
             the input image's on-disk dtype.
+
         Returns
         -------
         resampled : `spatialimage` or ndarray
             The data imaged after resampling to reference space.
+
         """
         if reference is not None and isinstance(reference, (str, Path)):
             reference = _nbload(str(reference))
@@ -388,5 +384,3 @@ def _as_homogeneous(xyz, dtype="float32", dim=3):
 def _apply_affine(x, affine, dim):
     """Get the image array's indexes corresponding to coordinates."""
     return affine.dot(_as_homogeneous(x, dim=dim).T)[:dim, ...].T
-
-#import pdb; pdb.set_trace()

From bafd2ed9a6248779c5c682a603d17baf9585457f Mon Sep 17 00:00:00 2001
From: Julien Marabotto <julienmarabotto@MacBook-Pro-de-Henri.local>
Date: Thu, 18 Apr 2024 17:06:23 +0200
Subject: [PATCH 12/14] enh: revert unrelated changes

---
 nitransforms/base.py   | 1 -
 nitransforms/linear.py | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/nitransforms/base.py b/nitransforms/base.py
index 117d4064..96f00edb 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -180,7 +180,6 @@ class TransformBase:
 
     __slots__ = ("_reference", "_ndim",)
 
-
     def __init__(self, reference=None):
         """Instantiate a transform."""
         self._reference = None
diff --git a/nitransforms/linear.py b/nitransforms/linear.py
index 569ac9c2..c7eb608a 100644
--- a/nitransforms/linear.py
+++ b/nitransforms/linear.py
@@ -275,7 +275,7 @@ def __repr__(self):
 
         """
         return repr(self.matrix)
-    
+
 
 class LinearTransformsMapping(Affine):
     """Represents a series of linear transforms."""
@@ -538,4 +538,4 @@ def load(filename, fmt=None, reference=None, moving=None):
     if isinstance(xfm, LinearTransformsMapping) and len(xfm) == 1:
         xfm = xfm[0]
 
-    return xfm
\ No newline at end of file
+    return xfm

From acb0736291a17dd3af46a25e2ca7efc65762b68e Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 19 Apr 2024 10:15:32 +0200
Subject: [PATCH 13/14] Update nitransforms/tests/test_base.py

---
 nitransforms/tests/test_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nitransforms/tests/test_base.py b/nitransforms/tests/test_base.py
index f315cc6c..07a7e4ec 100644
--- a/nitransforms/tests/test_base.py
+++ b/nitransforms/tests/test_base.py
@@ -111,7 +111,7 @@ def _to_hdf5(klass, x5_root):
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
     )
 
-    #Test ndim returned by affine
+    # Test ndim returned by affine
     assert nitl.Affine().ndim == 3
     assert nitl.LinearTransformsMapping(
         [nitl.Affine(), nitl.Affine()]

From 4a182000449165c45e3a8617ba15a8c079a576c3 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 19 Apr 2024 10:17:27 +0200
Subject: [PATCH 14/14] Update nitransforms/linear.py

---
 nitransforms/linear.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nitransforms/linear.py b/nitransforms/linear.py
index c7eb608a..af14f396 100644
--- a/nitransforms/linear.py
+++ b/nitransforms/linear.py
@@ -147,7 +147,7 @@ def matrix(self):
     def ndim(self):
         """Access the internal representation of this affine."""
         return self._matrix.ndim + 1
-    
+
     def map(self, x, inverse=False):
         r"""
         Apply :math:`y = f(x)`.