X5.py created

(cherry picked from commit 49bf4c3)

Author: Julien Marabotto

nitransforms/io/__init__.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Read and write transforms."""
-from nitransforms.io import afni, fsl, itk, lta
+from nitransforms.io import afni, fsl, itk, lta, x5
 from nitransforms.io.base import TransformIOError, TransformFileError
 
 __all__ = [
@@ -22,6 +22,7 @@
     "fs": (lta, "FSLinearTransform"),
     "fsl": (fsl, "FSLLinearTransform"),
     "afni": (afni, "AFNILinearTransform"),
+    "x5": (x5, "X5LinearTransform")
 }
 
 

nitransforms/io/x5.py

@@ -0,0 +1,53 @@
+"""Read/write x5 transforms."""
+import warnings
+import numpy as np
+from scipy.io import loadmat as _read_mat, savemat as _save_mat
+from h5py import File as H5File
+from nibabel import Nifti1Header, Nifti1Image
+from nibabel.affines import from_matvec
+from nitransforms.io.base import (
+    BaseLinearTransformList,
+    DisplacementsField,
+    LinearParameters,
+    TransformIOError,
+    TransformFileError,
+)
+
+LPS = np.diag([-1, -1, 1, 1])
+
+class X5LinearTransform(LinearParameters):
+    """A string-based structure for X5 linear transforms."""
+
+    template_dtype = np.dtype(
+        [
+            ("type", "i4"),
+            ("index", "i4"),
+            ("parameters", "f8", (4, 4)),
+            ("offset", "f4", 3),  # Center of rotation
+        ]
+    )
+    dtype = template_dtype
+
+    def __init__(self, parameters=None, offset=None):
+        return
+
+    def __str__(self):
+        return
+
+    def to_filename(self, filename):
+        """Store this transform to a file with the appropriate format."""
+        sa = self.structarr
+        affine = np.array(
+                np.hstack(
+                    (sa["parameters"][:3, :3].reshape(-1), sa["parameters"][:3, 3])
+                )[..., np.newaxis],
+                dtype="f8",
+            )
+        return
+    
+    @classmethod
+    def from_filename(cls, filename):
+        """Read the struct from a X5 file given its path."""
+        if str(filename).endswith(".h5"):
+            with H5File(str(filename)) as f:
+                return cls.from_h5obj(f)